An official website of the United States government
ABSTRACT In recent years, considerable progress has been made in topologically and functionally characterizing integral outer membrane proteins (OMPs) of Treponema pallidum subspecies pallidum , the syphilis spirochete, and identifying its surface-exposed β-barrel domains. Extracellular loops in OMPs of Gram-negative bacteria are known to be highly variable. We examined the sequence diversity of β-barrel-encoding regions of tprC , tprD , and bamA in 31 specimens from Cali, Colombia; San Francisco, California; and the Czech Republic and compared them to allelic variants in the 41 reference genomes in the NCBI database. To establish a phylogenetic framework, we used T. pallidum 0548 ( tp0548 ) genotyping and tp0558 sequences to assign strains to the Nichols or SS14 clades. We found that (i) β-barrels in clinical strains could be grouped according to allelic variants in T. pallidum subsp. pallidum reference genomes; (ii) for all three OMP loci, clinical strains within the Nichols or SS14 clades often harbored β-barrel variants that differed from the Nichols and SS14 reference strains; and (iii) OMP variable regions often reside in predicted extracellular loops containing B-cell epitopes. On the basis of structural models, nonconservative amino acid substitutions in predicted transmembrane β-strands of T. pallidum repeat C (TprC) and TprD2 could give rise to functional differences in their porin channels. OMP profiles of some clinical strains were mosaics of different reference strains and did not correlate with results from enhanced molecular typing. Our observations suggest that human host selection pressures drive T. pallidum subsp. pallidum OMP diversity and that genetic exchange contributes to the evolutionary biology of T. pallidum subsp. pallidum . They also set the stage for topology-based analysis of antibody responses to OMPs and help frame strategies for syphilis vaccine development. IMPORTANCE Despite recent progress characterizing outer membrane proteins (OMPs) of Treponema pallidum , little is known about how their surface-exposed, β-barrel-forming domains vary among strains circulating within high-risk populations. In this study, sequences for the β-barrel-encoding regions of three OMP loci, tprC , tprD , and bamA , in T. pallidum subsp. pallidum isolates from a large number of patient specimens from geographically disparate sites were examined. Structural models predict that sequence variation within β-barrel domains occurs predominantly within predicted extracellular loops. Amino acid substitutions in predicted transmembrane strands that could potentially affect porin channel function were also noted. Our findings suggest that selection pressures exerted within human populations drive T. pallidum subsp. pallidum OMP diversity and that recombination at OMP loci contributes to the evolutionary biology of syphilis spirochetes. These results also set the stage for topology-based analysis of antibody responses that promote clearance of T. pallidum subsp. pallidum and frame strategies for vaccine development based upon conserved OMP extracellular loops.
more »
« less
This content will become publicly available on May 20, 2026
Enzyme-constrained metabolic model of Treponema pallidum identified glycerol-3-phosphate dehydrogenase as an alternate electron sink
ABSTRACT Treponema pallidum, the causative agent of syphilis, poses a significant global health threat. Its strict reliance on host-derived nutrients and difficulties inin vitrocultivation have impeded detailed metabolic characterization. In this study, we present iTP251, the first genome-scale metabolic model ofT. pallidum, reconstructed and extensively curated to capture its unique metabolic features. These refinements included the curation of key reactions such as pyrophosphate-dependent phosphorylation and pathways for nucleotide synthesis, amino acid synthesis, and cofactor metabolism. The model demonstrated high predictive accuracy, validated by a MEMOTE score of 92%. To further enhance its predictive capabilities, we developed ec-iTP251, an enzyme-constrained version of iTP251, incorporating enzyme turnover rate and molecular weight information for all reactions having gene-protein-reaction associations. Ec-iTP251 provides detailed insights into protein allocation across carbon sources, showing strong agreement with proteomics data (Pearson’s correlation of 0.88) in the central carbon pathway. Moreover, the thermodynamic analysis revealed that lactate uptake serves as an additional ATP-generating strategy to utilize unused proteomes, albeit at the cost of reducing the driving force of the central carbon pathway by 27%. Subsequent analysis identified glycerol-3-phosphate dehydrogenase as an alternative electron sink, compensating for the absence of a conventional electron transport chain while maintaining cellular redox balance. These findings highlightT. pallidum’s metabolic adaptations for survival and redox balance in nutrient-limited, extracellular host environments, providing a foundation for future research into its unique bioenergetics. IMPORTANCEThis study advances our understanding ofTreponema pallidum, the syphilis-causing pathogen, through the reconstruction of iTP251, the first genome-scale metabolic model for this organism, and its enzyme-constrained version, ec-iTP251. The work addresses the challenges of studyingT. pallidum, an extracellular, host-adapted pathogen, due to its strict dependence on host-derived nutrients and challenges inin vitrocultivation. Validated with strong agreement to proteomics data, the model demonstrates high predictive reliability. Key insights include unique metabolic adaptations such as lactate uptake for ATP production and alternative redox-balancing mechanisms. These findings provide a robust framework for future studies aimed at unraveling the pathogen's survival strategies and identifying potential metabolic vulnerabilities.
more »
« less
- Award ID(s):
- 1943310
- PAR ID:
- 10595641
- Editor(s):
- Zhang, Ying
- Publisher / Repository:
- American Society for Microbiology
- Date Published:
- Journal Name:
- mSystems
- Volume:
- 10
- Issue:
- 5
- ISSN:
- 2379-5077
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
Kendall, Melissa M (Ed.)ABSTRACT Bacteria can change morphology in response to stressors and changes in their environment, including infection of a host. We previously identified the bacterial species,Bordetella atropi, which uses nutrient-induced filamentation as a novel mechanism for cell-to-cell spreading in the intestinal epithelial cells of a nematode host. To further investigate the conservation of nutrient-induced filamentation in Bordetellae, we utilized the turkey-infecting speciesBordetella avium,which filamentsin vitrowhen switched from a standard growth media to an enriched media. We conducted a selection-based filamentation screen withB. aviumand isolated two independent non-filamentous mutants that failed to filament in highly enriched media. These mutants contained different alleles inbvgS,the sensor in the two-component master virulence regulator (BvgAS) conserved across theBordetellagenus. To investigate the role ofbvgSin nutrient-induced filamentation, we conducted transcriptomics and found that our allele ofbvgSresulted in loss of responsiveness to highly enriched media, especially in genes related to nutrient uptake and metabolism. The most dysregulated gene in thebvgSmutant encoded for succinyl-CoA:acetate CoA-transferase, and we were able to regulate filamentation with exogenous metabolites up and downstream of this enzyme. These data suggest thatbvgSregulates nutrient-induced filamentation by controlling metabolic capacity. Overall, we found that the virulence regulatorbvgScan control nutrient-induced filamentation inB. avium,suggesting there may be conservation in Bordetellae for utilizing this morphological change as a virulence phenotype.IMPORTANCEBordetella aviumis the causative agent of bordetellosis, an infectious disease affecting the respiratory system of birds, significantly increasing morbidity in poultry, ultimately leading to economic losses. It is long known that the pathogenesis ofB. aviumis governed by the two-component master virulence regulator, BvgAS. However, this regulon has never before been associated with nutrient-induced filamentation. In this study, we identify BvgS to be regulating nutrient-induced filamentation. We also report the first transcriptomics analysis of filamentousB. avium, showing the enzyme succinyl-CoA:acetate CoA-transferase may be involved in a metabolic shift in enriched nutrient conditions leading to filamentation. Our results suggest that virulence inB. aviumis a dynamic relationship, affected by nutrient availability, rather than a simple binary decision.more » « less
-
Rudi, Knut (Ed.)ABSTRACT Functional studies of host-microbe interactions benefit from natural model systems that enable the exploration of molecular mechanisms at the host-microbe interface. BioluminescentVibrio fischericolonize the light organ of the Hawaiian bobtail squid,Euprymna scolopes, and this binary model has enabled advances in understanding host-microbe communication, colonization specificity,in vivobiofilms, intraspecific competition, and quorum sensing. The hummingbird bobtail squid,Euprymna berryi,can be generationally bred and maintained in lab settings and has had multiple genes deleted by CRISPR approaches. The prospect of expanding the utility of the light organ model system by producing multigenerational host lines led us to determine the extent to which theE. berryilight organ symbiosis parallels known processes inE. scolopes. However, the nature of theE. berryilight organ, including its microbial constituency and specificity for microbial partners, has not been examined. In this report, we isolated bacteria fromE. berryianimals and tank water. Assays of bacterial behaviors required in the host, as well as host responses to bacterial colonization, illustrate largely parallel phenotypes inE. berryiandE. scolopeshatchlings. This study revealsE. berryito be a valuable comparative model to complement studies inE. scolopes.IMPORTANCEMicrobiome studies have been substantially advanced by model systems that enable functional interrogation of the roles of the partners and the molecular communication between those partners. TheEuprymna scolopes-Vibrio fischerisystem has contributed foundational knowledge, revealing key roles for bacterial quorum sensing broadly and in animal hosts, for bacteria in stimulating animal development, for bacterial motility in accessing host sites, and forin vivobiofilm formation in development and specificity of an animal’s microbiome.Euprymna berryiis a second bobtail squid host, and one that has recently been shown to be robust to laboratory husbandry and amenable to gene knockout. This study identifiesE. berryias a strong symbiosis model host due to features that are conserved with those ofE. scolopes, which will enable the extension of functional studies in bobtail squid symbioses.more » « less
-
Nikel, Pablo Ivan (Ed.)ABSTRACT The bacteriumAcinetobacter baylyiis a model organism known for its extreme natural competence and metabolic versatility. It is capable of taking up environmental DNA at a high rate across all growth phases. The type strain ADP1 was created by random mutagenesis of a precursor strain, BD4, to prevent it from forming cell chains in culture. ADP1 has since been distributed between research groups over several decades and acquired subsequent mutations during this time. In this study, we compare the genome sequences ofA. baylyiBD4 and its modern descendants to identify and understand the effects of mutations acquired and engineered during its domestication. We demonstrate that the ADP1 variants in use today differ in their competence, growth on different carbon sources, and autoaggregation. In addition, we link the global carbon storage regulator CsrA and a transposon insertion that removes its C-terminal domain specifically to changes in both overall competence and an almost complete loss of competence during the stationary phase. Reconstructing the history of ADP1 and the diversity that has evolved in the variants currently in use improves our understanding of the desirable properties of this experimentally and industrially important bacterium and suggests ways that its reliability can be improved through further genome engineering.IMPORTANCEAcinetobacter baylyiADP1 is a bacterial chassis of interest to microbiologists in academia and industry due to its extreme natural competence and wide metabolic range. Its ability to take up DNA from its environment makes it straightforward to efficiently edit its chromosome. We identify and characterize mutations that have been passed down to modern strains of ADP1 from the initial work in the 1960s, as well as subsequent mutations and genome edits separating strains in use by different research groups today. These mutations, including one in a global regulator (CsrA), have significant phenotypic consequences that have affected the reproducibility and consistency of experiments reported in the literature. We link a mutation in this global regulator to unexpected changes in natural competence. We also show that domesticatedA. baylyistrains have impaired growth on a variety of carbon sources.more » « less
-
Tischler, Dirk (Ed.)ABSTRACT Space missions or spacecraft equipment destined for sensitive environments, such as Mars, Europa, or Enceladus, are required to be designed to avoid forward contamination. Spacecraft are assembled in clean rooms (SACs) employing treatments to eliminate microbial contamination. However, some organisms can survive the cleaning procedures. Characterization of these populations, through both culture-based and sequencing methods, reveals that the majority consists of spore-forming bacteria. However, a smaller group of non-spore-forming organisms, primarily classified within the orderMicrococcalesof the phylumActinobacteria(Actinomycetota), exists in some SACs. Despite their repeated occurrence and isolation, actinobacterial strains associated with SACs have not been studied for their dormancy potential. Here, we show for the first time that a non-spore-forming SAC isolate,Tersicoccus phoenicis(Micrococcales), enters dormancy under nutrient starvation. Dormancy inMicrococcus luteusinvolves a universal stress protein and a resuscitation-promoting factor (Rpf). Genes for these proteins are widely found in actinobacteria, includingT. phoenicis. We show that dormantT. phoenicis(Micrococcales) can be revived through the addition of the Rpf to the media. Dormancy, as observed in the SAC actinobacterial isolateT. phoenicis, could well be a common trait adopted by other actinobacterial strains under the stressful conditions of spacecraft clean rooms or the ISS (International Space Station). This has implications for the persistence, identification, and recovery of such microbes from cleanroom facilities.IMPORTANCENASA’s long-range goal of a human mission to the Mars surface raises issues relating to planetary protection. The concerns of forward contamination require that spacecraft assembly clean rooms (SACs) be maintained to inhibit microbial survival. However, despite these efforts, distinct microbial communities persist. Here, we show that a SAC isolate,T. phoenicis, exhibits dormancy, a state in which the cells are viable but not cultivable. Dormancy may help non-spore-forming organisms survive in the clean room environments utilized for space missions. This has implications for improving cleaning procedures.more » « less
