Cryo-electron tomography reveals the binding and release states of the major adhesion complex from Mycoplasma genitalium.

The nap particle is an immunogenic surface adhesion complex from Mycoplasma genitalium. It is essential for motility and responsible for binding sialylated oligosaccharides on the surface of the host cell. The nap particle is composed of two P140-P110 heterodimers, the structure of which was recently solved. However, the interpretation of the mechanism by which the mycoplasma cells orchestrate adhesion remained challenging. Here, we provide cryo-electron tomography structures at ~11 Å resolution, which allow for the distinction between the bound and released state of the nap particle, displaying the in vivo conformational states. Fitting of the atomically resolved structures reveals that bound sialylated oligosaccharides are stabilized by both P110 and P140. Movement of the stalk domains allows for the transfer of conformational changes from the interior of the cell to the binding pocket, thus having the capability of an active release process. It is likely that the same mechanism can be transferred to other Mycoplasma species that belong to the pneumoniae cluster.

The adhesion protein of Mycoplasma genitalium inhibits urethral epithelial cell apoptosis through CypA-CD147 activating PI3K/ Akt/NF-κB pathway.

By interacting with the receptor on the host cells membrane, Mycoplasma genitalium, a prokaryotic bacterium primarily transmitted through sexual contact, can adhere to and even enter cells. The adhesion protein of M. genitalium (MgPa) plays a critical function in the adhering and subsequent invasion into host cells. Our prior studies verified that cyclophilin A (CypA) was the receptor of MgPa on human urethral epithelial cells (SV-HUC-1) membrane and could induce pro-inflammatory cytokines production through the CypA-CD147-ERK-NF-κB pathway. This research aims to understand how MgPa interacts with its membrane receptor CypA to cause apoptosis in host cells. We employed flow cytometry to see if MgPa prevents or enhances apoptosis of SV-HUC-1 cells. The apoptosis-related proteins such as Bax, caspase-3, and cleaved caspase-3 were assayed using Western blot. Results suggested that MgPa could inhibit the apoptosis of SV-HUC-1 cells. And we demonstrated that interference with the expression of CypA or CD147 significantly reversed the inhibitory effect of MgPa on SV-HUC-1 cells apoptosis, indicating that MgPa inhibited urothelial cells apoptosis through CypA/CD147. Furthermore, we discovered that MgPa regulates the PI3K/Akt/NF-κB pathway through CypA/CD147 to inhibit SV-HUC-1 cells apoptosis. Ultimately, the inhibitory effect of MgPa on the apoptosis of the urothelial epithelial cells extracted from CypA-knockout mice was validated by Annexin V/PI assay. The results corroborated that MgPa could also inhibit mouse urothelial epithelial cells apoptosis. In summary, we demonstrated that MgPa could inhibit SV-HUC-1 cells apoptosis via regulating the PI3K/Akt/NF-κB pathway through CypA/CD147, providing experimental evidence for elucidating the survival strategies of M. genitalium in host cells. KEY POINTS: • M. genitalium protein of adhesion inhibited human urethral epithelial cells apoptosis through CypA-CD147 activating the signal pathway of PI3K/Akt/NF-κB • The knockdown of CypA and CD147 could downregulate the M. genitalium -activated PI3K/Akt/NF-κB pathway in SV-HUC-1 cells • MgPa could inhibit the apoptosis of normal C57BL mouse primary urethral epithelial cells, but not for CypA-knockout C57BL mouse primary urethral epithelial cells.

Identification of histone H2B as a potential receptor for Mycoplasma genitalium protein of adhesion.

Mycoplasma genitalium, the smallest prokaryotic microorganism capable of independent replication, is increasingly recognized as a sexually transmitted pathogen. M. genitalium protein of adhesion (MgPa) plays a pivotal role in the process of M. genitalium adhesion to host cells. We previously identified cyclophilin A as a cellular receptor of MgPa using the virus overlay protein binding assay (VOPBA) together with liquid chromatography-mass spectrometry (LC-MS). In the current study, we have evaluated H2B as an alternative cellular receptor for MgPa since H2B was assigned the second higher score as a potential binding partner of MgPa in the VOPBA and LC-MS screen. It was found that recombinant MgPa specifically bind to H2B both in the SV-HUC-1 cell membrane and in form of a recombinant protein. H2B was detected throughout the SV-HUC-1 cells, including the cytoplasmic membrane, cytosol and nucleus. Importantly, H2B partially inhibited the adhesion of M. genitalium to SV-HUC-1 cells. Finally, H2B was both co-precipitated with recombinant MgPa and co-localized with M. genitalium and recombinant MgPa in SV-HUC-1 cells. The above observations suggest that H2B may act as a potential cellular receptor of MgPa for mediating M. genitalium adhesion to host cells.

The Sialoglycan Binding Adhesins of Mycoplasma genitalium and Mycoplasma pneumoniae.

Mycoplasma genitalium (Mge) and Mycoplasma pneumoniae (Mpn) are two human pathogens associated with urogenital and respiratory tract infections, respectively. The recent elucidation of the tridimensional structure of their major cytoadhesins by X-ray crystallography and cryo-electron microscopy/tomography, has provided important insights regarding the mechanics of infection and evasion of immune surveillance.

A biochemical network modeling of a whole-cell.

All cellular processes can be ultimately understood in terms of respective fundamental biochemical interactions between molecules, which can be modeled as networks. Very often, these molecules are shared by more than one process, therefore interconnecting them. Despite this effect, cellular processes are usually described by separate networks with heterogeneous levels of detail, such as metabolic, protein-protein interaction, and transcription regulation networks. Aiming at obtaining a unified representation of cellular processes, we describe in this work an integrative framework that draws concepts from rule-based modeling. In order to probe the capabilities of the framework, we used an organism-specific database and genomic information to model the whole-cell biochemical network of the Mycoplasma genitalium organism. This modeling accounted for 15 cellular processes and resulted in a single component network, indicating that all processes are somehow interconnected. The topological analysis of the network showed structural consistency with biological networks in the literature. In order to validate the network, we estimated gene essentiality by simulating gene deletions and compared the results with experimental data available in the literature. We could classify 212 genes as essential, being 95% of them consistent with experimental results. Although we adopted a relatively simple organism as a case study, we suggest that the presented framework has the potential for paving the way to more integrated studies of whole organisms leading to a systemic analysis of cells on a broader scale. The modeling of other organisms using this framework could provide useful large-scale models for different fields of research such as bioengineering, network biology, and synthetic biology, and also provide novel tools for medical and industrial applications.

Structure and mechanism of the Nap adhesion complex from the human pathogen Mycoplasma genitalium.

Mycoplasma genitalium is a human pathogen adhering to host target epithelial cells and causing urethritis, cervicitis and pelvic inflammatory disease. Essential for infectivity is a transmembrane adhesion complex called Nap comprising proteins P110 and P140. Here we report the crystal structure of P140 both alone and in complex with the N-terminal domain of P110. By cryo-electron microscopy (cryo-EM) and tomography (cryo-ET) we find closed and open Nap conformations, determined at 9.8 and 15 Å, respectively. Both crystal structures and the cryo-EM structure are found in a closed conformation, where the sialic acid binding site in P110 is occluded. By contrast, the cryo-ET structure shows an open conformation, where the binding site is accessible. Structural information, in combination with functional studies, suggests a mechanism for attachment and release of M. genitalium to and from the host cell receptor, in which Nap conformations alternate to sustain motility and guarantee infectivity.

The association of Chlamydia trachomatis and Mycoplasma genitalium infection with the vaginal metabolome.

Chlamydia trachomatis (CT) and Mycoplasma genitalium (MG) are two highly prevalent bacterial sexually transmitted infections (STIs) with a significant rate of co-infection in some populations. Vaginal metabolites are influenced by resident vaginal microbiota, affect susceptibility to sexually transmitted infections (STIs), and may impact local inflammation and patient symptoms. Examining the vaginal metabolome in the context of CT mono (CT+) and CT/MG co-infection (CT+/MG+) may identify biomarkers for infection or provide new insights into disease etiology and pathogenesis. Yet, the vaginal metabolome in the setting of CT infection is understudied and the composition of the vaginal metabolome in CT/MG co-infected women is unknown. Therefore, in this analysis, we used an untargeted metabolomic approach combined with 16S rRNA gene amplicon sequencing to characterize the vaginal microbiota and metabolomes of CT+, CT+/MG+, and uninfected women. We found that CT+ and CT+/MG+ women had distinct vaginal metabolomic profiles as compared to uninfected women both before and after adjustment for the vaginal microbiota. This study provides important foundational data documenting differences in the vaginal metabolome between CT+, CT+/MG+ and uninfected women. These data may guide future mechanistic studies that seek to provide insight into the pathogenesis of CT and CT/MG infections.

Transcriptional response to metal starvation in the emerging pathogen Mycoplasma genitalium is mediated by Fur-dependent and -independent regulatory pathways.

Transition metals participate in numerous enzymatic reactions and they are essential for survival in all living organisms. For this reason, bacterial pathogens have evolved dedicated machineries to effectively compete with their hosts and scavenge metals at the site of infection. In this study, we investigated the mechanisms controlling metal acquisition in the emerging human pathogen Mycoplasma genitalium. We observed a robust transcriptional response to metal starvation, and many genes coding for predicted lipoproteins and ABC-transporters were significantly up-regulated. Transcriptional analysis of a mutant strain lacking a metalloregulator of the Fur family revealed the activation of a full operon encoding a putative metal transporter system and a gene coding for a Histidine-rich lipoprotein (Hrl). We recognized a conserved sequence with dyad symmetry within the promoter region of the Fur-regulated genes. Mutagenesis of the predicted Fur operator within the hrl promoter abrogated Fur- and metal-dependent expression of a reporter gene. Metal starvation still impelled a strong transcriptional response in the fur mutant, demonstrating the existence of Fur-independent regulatory pathways controlling metal homeostasis. Finally, analysis of metal accumulation in the wild-type strain and the fur mutant by ICP-MS revealed an important role of Fur in nickel acquisition.

Three polypeptides screened from phage display random peptide library may be the receptor polypeptide of Mycoplasma genitalium adhesion protein.

Mycoplasma genitalium adhesion protein (MgPa) is a major adhesin of M. genitalium, a human pathogen associated with a series of genitourinary tract diseases. MgPa plays a very important role in M. genitalium adhering to the host cells. However, the exact receptor peptides or proteins of MgPa are still poorly understood so far. Three polypeptides (V-H-W-D-F-R-Q-W-W-Q-P-S), (D-W-S-S-W-V -Y-R-D-P-Q-T) and (H-Y-I-D-F-R-W) were previously screened from a phage display random peptide library using recombinant MgPa (rMgPa) as a target molecule. In this study, three polypeptides were artificially synthesized and investigated as to whether they are potential receptors of MgPa. We found that rMgPa specifically bound to three synthesized polypeptides as determined via an indirect enzyme-linked immunosorbent assay (ELISA). Moreover, three polypeptides were further identified by indirect immunofluorescence microscopy (IFM). We confirmed that rMgPa and M. genitalium can adhere to SV-HUC-1 cells in vitro and that anti-rMgPa antibody and three synthesized polypeptides can partially inhibit the adherence of rMgPa and M. genitalium to SV-HUC-1 cells. In summary, these three polypeptides may be the essential receptor peptides of MgPa, and may aid in enhancing the understanding of biological function of MgPa and the possible pathogenic mechanism of M. genitalium.

Activation of σ20-dependent recombination and horizontal gene transfer in Mycoplasma genitalium.

In the human pathogen Mycoplasma genitalium, homologous recombination is under the control of σ20, an alternative sigma factor that boosts the generation of genetic and antigenic diversity in the population. Under laboratory growth conditions, σ20 activation is rare and the factors governing its intermittent activity are unknown. Two σ20-regulated genes, rrlA and rrlB, showed to be important for recombination of homologous DNA sequences in this bacterium. Herein, we demonstrate that rrlA and rrlB code for two small proteins that participate in a feed-forward loop essential for σ20 function. In addition, we identify novel genes regulated by σ20 and show that several non-coding regions, which function as a reservoir for the generation of antigenic diversity, are also activated by this alternative sigma factor. Finally, we reveal that M. genitalium cells can transfer DNA horizontally by a novel mechanism that requires RecA and is facilitated by σ20 over-expression. This DNA transfer system is arguably fundamental for persistence of M. genitalium within the host since it could facilitate a rapid dissemination of successful antigenic variants within the population. Overall, these findings impose a novel conception of genome evolution, genetic variation and survival of M. genitalium within the host.

The nucleotide-bound/substrate-bound conformation of the Mycoplasma genitalium DnaK chaperone.

Hsp70 chaperones keep protein homeostasis facilitating the response of organisms to changes in external and internal conditions. Hsp70s have two domains-nucleotide binding domain (NBD) and substrate binding domain (SBD)-connected by a conserved hydrophobic linker. Functioning of Hsp70s depend on tightly regulated cycles of ATP hydrolysis allosterically coupled, often together with cochaperones, to the binding/release of peptide substrates. Here we describe the crystal structure of the Mycoplasma genitalium DnaK (MgDnaK) protein, an Hsp70 homolog, in the noncompact, nucleotide-bound/substrate-bound conformation. The MgDnaK structure resembles the one from the thermophilic eubacteria DnaK trapped in the same state. However, in MgDnaK the NBD and SBD domains remain close to each other despite the lack of direct interaction between them and with the linker contacting the two subdomains of SBD. These observations suggest that the structures might represent an intermediate of the protein where the conserved linker binds to the SBD to favor the noncompact state of the protein by stabilizing the SBDß-SBDα subdomains interaction, promoting the capacity of the protein to sample different conformations, which is critical for proper functioning of the molecular chaperone allosteric mechanism. Comparison of the solved structures indicates that the NBD remains essentially invariant in presence or absence of nucleotide.

Macrolide resistance in Mycoplasma genitalium from female sex workers in Belgium.

OBJECTIVES: Mycoplasma genitalium is emerging as an aetiological agent of sexually transmitted infections (STIs). Although M. genitalium is commonly treated with azithromycin, macrolide resistance associated with point mutations in the 23S rRNA gene is emerging. METHODS: In this study, the prevalence of M. genitalium and macrolide resistance in female sex workers (FSW) in Belgium was evaluated by a prospective study conducted between 2015 and 2016. Vaginal swabs were sampled from 303 FSW who underwent testing for M. genitalium along with standard STI screening. All samples positive for M. genitalium were subsequently tested for mutations associated with macrolide resistance. RESULTS: M. genitalium was detected in 10.8% of participants and macrolide resistance-associated mutations (A2058G and A2059G) were found in 6.5% of isolates. CONCLUSIONS: M. genitalium is clearly present in FSW in Belgium. In contrast to other reports, for now the occurrence of macrolide resistance appears limited in this specific target population.

Structural characterization of the NAP; the major adhesion complex of the human pathogen Mycoplasma genitalium.

Mycoplasma genitalium, the causative agent of non-gonococcal urethritis and pelvic inflammatory disease in humans, is a small eubacterium that lacks a peptidoglycan cell wall. On the surface of its plasma membrane is the major surface adhesion complex, known as NAP that is essential for adhesion and gliding motility of the organism. Here, we have performed cryo-electron tomography of intact cells and detergent permeabilized M. genitalium cell aggregates, providing sub-tomogram averages of free and cell-attached NAPs respectively, revealing a tetrameric complex with two-fold rotational (C2) symmetry. Each NAP has two pairs of globular lobes (named α and ß lobes), arranged as a dimer of heterodimers with each lobe connected by a stalk to the cell membrane. The ß lobes are larger than the α lobes by 20%. Classification of NAPs showed that the complex can tilt with respect to the cell membrane. A protein complex containing exclusively the proteins P140 and P110, was purified from M. genitalium and was structurally characterized by negative-stain single particle EM reconstruction. The close structural similarity found between intact NAPs and the isolated P140/P110 complexes, shows that dimers of P140/P110 heterodimers are the only components of the extracellular region of intact NAPs in M. genitalium.

Improved Metabolic Models for E. coli and Mycoplasma genitalium from GlobalFit, an Algorithm That Simultaneously Matches Growth and Non-Growth Data Sets.

Constraint-based metabolic modeling methods such as Flux Balance Analysis (FBA) are routinely used to predict the effects of genetic changes and to design strains with desired metabolic properties. The major bottleneck in modeling genome-scale metabolic systems is the establishment and manual curation of reliable stoichiometric models. Initial reconstructions are typically refined through comparisons to experimental growth data from gene knockouts or nutrient environments. Existing methods iteratively correct one erroneous model prediction at a time, resulting in accumulating network changes that are often not globally optimal. We present GlobalFit, a bi-level optimization method that finds a globally optimal network, by identifying the minimal set of network changes needed to correctly predict all experimentally observed growth and non-growth cases simultaneously. When applied to the genome-scale metabolic model of Mycoplasma genitalium, GlobalFit decreases unexplained gene knockout phenotypes by 79%, increasing accuracy from 87.3% (according to the current state-of-the-art) to 97.3%. While currently available computers do not allow a global optimization of the much larger metabolic network of E. coli, the main strengths of GlobalFit are already played out when considering only one growth and one non-growth case simultaneously. Application of a corresponding strategy halves the number of unexplained cases for the already highly curated E. coli model, increasing accuracy from 90.8% to 95.4%.

Structure-Guided Mutations in the Terminal Organelle Protein MG491 Cause Major Motility and Morphologic Alterations on Mycoplasma genitalium.

The emergent human pathogen Mycoplasma genitalium, with one of the smallest genomes among cells capable of growing in axenic cultures, presents a flask-shaped morphology due to a protrusion of the cell membrane, known as the terminal organelle, that is involved in cell adhesion and motility and is an important virulence factor of this microorganism. The terminal organelle is supported by a cytoskeleton complex of about 300 nm in length that includes three substructures: the terminal button, the rod and the wheel complex. The crystal structure of the MG491 protein, a proposed component of the wheel complex, has been determined at ~3 Å resolution. MG491 subunits are composed of a 60-residue N-terminus, a central three-helix-bundle spanning about 150 residues and a C-terminal region that appears to be quite flexible and contains the region that interacts with MG200, another key protein of the terminal organelle. The MG491 molecule is a tetramer presenting a unique organization as a dimer of asymmetric pairs of subunits. The asymmetric arrangement results in two very different intersubunit interfaces between the central three-helix-bundle domains, which correlates with the formation of only ~50% of the intersubunit disulfide bridges of the single cysteine residue found in MG491 (Cys87). Moreover, M. genitalium cells with a point mutation in the MG491 gene causing the change of Cys87 to Ser present a drastic reduction in motility (as determined by microcinematography) and important alterations in morphology (as determined by electron microscopy), while preserving normal levels of the terminal organelle proteins. Other variants of MG491, designed also according to the structural information, altered significantly the motility and/or the cell morphology. Together, these results indicate that MG491 plays a key role in the functioning, organization and stabilization of the terminal organelle.

Systems biology definition of the core proteome of metabolism and expression is consistent with high-throughput data.

Finding the minimal set of gene functions needed to sustain life is of both fundamental and practical importance. Minimal gene lists have been proposed by using comparative genomics-based core proteome definitions. A definition of a core proteome that is supported by empirical data, is understood at the systems-level, and provides a basis for computing essential cell functions is lacking. Here, we use a systems biology-based genome-scale model of metabolism and expression to define a functional core proteome consisting of 356 gene products, accounting for 44% of the Escherichia coli proteome by mass based on proteomics data. This systems biology core proteome includes 212 genes not found in previous comparative genomics-based core proteome definitions, accounts for 65% of known essential genes in E. coli, and has 78% gene function overlap with minimal genomes (Buchnera aphidicola and Mycoplasma genitalium). Based on transcriptomics data across environmental and genetic backgrounds, the systems biology core proteome is significantly enriched in nondifferentially expressed genes and depleted in differentially expressed genes. Compared with the noncore, core gene expression levels are also similar across genetic backgrounds (two times higher Spearman rank correlation) and exhibit significantly more complex transcriptional and posttranscriptional regulatory features (40% more transcription start sites per gene, 22% longer 5'UTR). Thus, genome-scale systems biology approaches rigorously identify a functional core proteome needed to support growth. This framework, validated by using high-throughput datasets, facilitates a mechanistic understanding of systems-level core proteome function through in silico models; it de facto defines a paleome.

Summary of the DREAM8 Parameter Estimation Challenge: Toward Parameter Identification for Whole-Cell Models.

Whole-cell models that explicitly represent all cellular components at the molecular level have the potential to predict phenotype from genotype. However, even for simple bacteria, whole-cell models will contain thousands of parameters, many of which are poorly characterized or unknown. New algorithms are needed to estimate these parameters and enable researchers to build increasingly comprehensive models. We organized the Dialogue for Reverse Engineering Assessments and Methods (DREAM) 8 Whole-Cell Parameter Estimation Challenge to develop new parameter estimation algorithms for whole-cell models. We asked participants to identify a subset of parameters of a whole-cell model given the model's structure and in silico "experimental" data. Here we describe the challenge, the best performing methods, and new insights into the identifiability of whole-cell models. We also describe several valuable lessons we learned toward improving future challenges. Going forward, we believe that collaborative efforts supported by inexpensive cloud computing have the potential to solve whole-cell model parameter estimation.

[Mycoplasma genitalium-derived lipid-associated membrane proteins negatively regulate cytokine secretion by inducing HO-1 expression in placental trophoblast cells].

OBJECTIVE: To observe the expression of heme oxygenase-1 (HO-1) in regulation of cytokines response induced by Mycoplasma genitalium-derived lipid-associated membrane proteins (LAMPs) in placental trophoblast cells. METHODS: Placental trophoblast cells were cultured in vitro and stimulated by 0.5-5 µg/mL LAMPs for 4 to 12 hours. Expression of HO-1 mRNA and protein, and nuclear translocation of nuclear factor erythroid-2 related factor 2 (Nrf2) were detected by real-time quantitative PCR and Western blotting, respectively. The intracellular formation of reactive oxygen species (ROS) was detected by the fluorescent probe H2DCFDA. N-acetyl-cysteine (NAC) and nuclear factor erythroid-2 related factor 2 (Nrf2) siRNA were respectively used to analyze the roles of ROS and Nrf2 in mediating HO-1 expression. Finally, placental trophoblast cells were transfected with HO-1 siRNA, or preincubated by the HO-1 agonist cobalt protoporphyrin (CoPP) or its inhibitor zinc protoporphyrin (ZnPP), and LAMPs-induced secretion of TNF-α and IL-1ß were detected by ELISA. RESULTS: M. genitalium LAMPs induced the expression of HO-1 mRNA and protein, the accumulation of ROS and the nuclear translocation of Nrf2 in placental trophoblast cells. NAC treatment inhibited LAMPs-induced HO-1 expression and Nrf2 nuclear translocation, and the transfection of Nrf2 siRNA significantly abrogated HO-1 expression. Furthermore, HO-1 siRNA and ZnPP treatment increased LAMPs-induced TNF-α and IL-1ß secretion, while the HO-1 agonist CoPP treatment further decreased their production. CONCLUSION: M. genitalium LAMPs could induce placental trophoblast cells to express HO-1 through ROS/Nrf2 pathways. Up-regulation of HO-1 negatively regulates excessive production of cytokines.

Binding of CD14 to Mycoplasma genitalium-derived lipid-associated membrane proteins upregulates TNF-α.

Lipid-associated membrane proteins (LAMPs) are a mixture of mycoplasmal lipoproteins expressed on the surface, and they are the main structures for interaction with the host cells. The objective of this study was to explore the role of CD14 in immune recognition of Mycoplasma genitalium-derived LAMPs and investigate whether the binding of CD14 to LAMPs affects the inflammatory response. Enzyme-linked immunosorbent assay (ELISA), transient co-transfection, dual-luciferase reporter assay, specific inhibition assay, and competitive inhibition ELISA (CI-ELISA) were used. CD14 was involved in LAMP-stimulated production of tumor necrosis factor (TNF)-α by blocking CD14 antibody in THP-1 cells. Co-transfection experiments in HeLa cells provide evidence that CD14 facilitates LAMP-induced TNF-α release via toll-like receptor 2 (TLR2). In addition, LAMP-induced TNF-α release was increased by soluble CD14 but decreased by soluble TLR2. Lipid moieties of LAMPs pre-treated with lipoprotein lipase were responsible for TNF-α production. The binding of CD14 to LAMPs was supported by binding assay and CI-ELISA. Thus, we provide evidences that CD14 is not only able to recognize LAMPs but also its binding to LAMPs upregulates TNF-α release. These findings provide insight into the function of CD14 and the pathogenesis of mycoplasmal infections.