Phylogenetic Analysis of Chlamydia trachomatis Tarp and Correlation with Clinical Phenotype

ABSTRACT Chlamydia trachomatis is the leading cause of infectious blindness worldwide and is the most commonly reported pathogen causing sexually transmitted infections. Tarp (translocated actin recruiting phosphoprotein), a type III secreted effector that mediates actin nucleation, is central to C. trachomatis infection. The phylogenetic analysis of tarP from reference strains as well as ocular, genital, and lymphogranuloma venereum (LGV) clinical isolates demonstrated an evolutionary relationship with disease phenotype, with LGV and ocular isolates branched into clades that were separate from the urogenital isolates. The sequence analysis of Tarp indicated a high degree of variability and identified trends within clinical groupings. Tarps from LGV strains contained the highest number of tyrosine-rich repeat regions (up to nine) and the fewest (two) predicted actin binding domains. The converse was noted for Tarp proteins from ocular isolates that contained up to four actin binding domains and as few as one tyrosine-rich repeat region. The results suggest that Tarp is among the few known genes to play a role in C. trachomatis adaptations to specific niches within the host.

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Fluorescence-Reported Allelic Exchange Mutagenesis-Mediated Gene Deletion Indicates a Requirement for Chlamydia trachomatis Tarp during In Vivo Infectivity and Reveals a Specific Role for the C Terminus during Cellular Invasion

Infection and Immunity ◽

10.1128/iai.00841-19 ◽

2020 ◽

Vol 88 (5) ◽

Author(s):

Susmita Ghosh ◽

Elizabeth A. Ruelke ◽

Joshua C. Ferrell ◽

Maria D. Bodero ◽

Kenneth A. Fields ◽

...

Keyword(s):

Chlamydia Trachomatis ◽

Host Cell ◽

Host Cells ◽

Actin Binding ◽

Wild Type ◽

Content Type ◽

Allelic Exchange ◽

Binding Domains

ABSTRACT The translocated actin recruiting phosphoprotein (Tarp) is a multidomain type III secreted effector used by Chlamydia trachomatis. In aggregate, existing data suggest a role of this effector in initiating new infections. As new genetic tools began to emerge to study chlamydial genes in vivo, we speculated as to what degree Tarp function contributes to Chlamydia’s ability to parasitize mammalian host cells. To address this question, we generated a complete tarP deletion mutant using the fluorescence-reported allelic exchange mutagenesis (FRAEM) technique and complemented the mutant in trans with wild-type tarP or mutant tarP alleles engineered to harbor in-frame domain deletions. We provide evidence for the significant role of Tarp in C. trachomatis invasion of host cells. Complementation studies indicate that the C-terminal filamentous actin (F-actin)-binding domains are responsible for Tarp-mediated invasion efficiency. Wild-type C. trachomatis entry into HeLa cells resulted in host cell shape changes, whereas the tarP mutant did not. Finally, using a novel cis complementation approach, C. trachomatis lacking tarP demonstrated significant attenuation in a murine genital tract infection model. Together, these data provide definitive genetic evidence for the critical role of the Tarp F-actin-binding domains in host cell invasion and for the Tarp effector as a bona fide C. trachomatis virulence factor.

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Phylogenetic Characterization of the Palyam Serogroup Orbiviruses

Viruses ◽

10.3390/v11050446 ◽

2019 ◽

Vol 11 (5) ◽

pp. 446 ◽

Cited By ~ 3

Author(s):

Karen Ebersohn ◽

Peter Coetzee ◽

Louwrens P. Snyman ◽

Robert Swanepoel ◽

Estelle H. Venter

Keyword(s):

Phylogenetic Analysis ◽

Sequence Data ◽

Evolutionary Relationship ◽

Full Genome Sequence ◽

African Horse Sickness Virus ◽

Gene Encoding ◽

Phylogenetic Characterization ◽

Next Generation Sequencing Ngs ◽

High Degree

The Palyam serogroup orbiviruses are associated with abortion and teratogenesis in cattle and other ruminants. Of the 13 different serotypes that have been identified, the full genome sequence of only one, Kasba, has been published. We undertook to perform Next Generation Sequencing (NGS) and phylogenetic analysis on 12 Palyam serotypes plus field isolates of the African serotypes in our possession. The Palyam serogroup was found to be most closely related to the African horse sickness virus group and showed the most distant evolutionary relationship to the equine encephalosis viruses (EEV). Amino acid sequence analysis revealed that the gene encoding VP7 was the most conserved within serotypes and VP2 and VP5 showed the highest degree of variation. A high degree of sequence identity was found for isolates from the same geographical region. The phylogenetic analysis revealed two clades where the African serotypes were all very closely related in one clade and the other clade contained the Australian and Asian serotypes and one African serotype, Petevo. It was evident from the sequence data that the geographical origin of Palyam serogroup viruses played an important role in the development of the different serotypes.

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Hepatitis C: sexual or intrafamilial transmission? Epidemiological and phylogenetic analysis of hepatitis C virus in 24 infected couples

Revista da Sociedade Brasileira de Medicina Tropical ◽

10.1590/s0037-86822009000300001 ◽

2009 ◽

Vol 42 (3) ◽

pp. 239-244 ◽

Cited By ~ 17

Author(s):

Norma de Paula Cavalheiro ◽

Abel De La Rosa ◽

Slava Elagin ◽

Fátima Mitiko Tengan ◽

Evaldo Stanislau Affonso de Araújo ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Hepatitis C Virus ◽

Hepatitis C ◽

Virus Transmission ◽

Virus Genome ◽

Personal Hygiene ◽

Intrafamilial Transmission ◽

Sexually Transmitted ◽

High Degree

The role of sexual or intrafamilial transmission of hepatitis C is controversial. A phylogenetic analysis was performed on the non-structural region 5B of the hepatitis C virus (NS5B-HCV). High percentages of homology (mean of 98.3%) were shown between the couples. Twenty (83.3%) of the 24 men but only two of the women (8.3%) reported having had sexually transmitted diseases during their lives. The risk factors for HCV acquisition were blood transfusion (10 couples), use of illegal injected drugs (17), use of inhalants (15), acupuncture (5) and tattoos (5). The shared use of personal hygiene items included toothbrushes between six couples (25%), razor blades between 16 (66.7%), nail clippers between 21 (87.5%) and manicure pliers between 14 (58.3%). The high degree of similarity of the hepatitis C virus genome supports the hypothesis of hepatitis C virus transmission between these couples. The shared use of personal hygiene items suggests the possibility of intrafamilial transmission of infection.

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Is geography an accurate predictor of evolutionary history in the millipede family Xystodesmidae?

PeerJ ◽

10.7717/peerj.3854 ◽

2017 ◽

Vol 5 ◽

pp. e3854 ◽

Cited By ~ 1

Author(s):

Jackson C. Means ◽

Paul E. Marek

Keyword(s):

Phylogenetic Analysis ◽

Phylogenetic Relationships ◽

Bayes Factor ◽

Evolutionary Relationship ◽

Morphological Data ◽

Geographical Distance ◽

Molecular Topology ◽

The Family ◽

High Degree ◽

The Impact

For the past several centuries, millipede taxonomists have used the morphology of male copulatory structures (modified legs called gonopods), which are strongly variable and suggestive of species-level differences, as a source to understand taxon relationships. Millipedes in the family Xystodesmidae are blind, dispersal-limited and have narrow habitat requirements. Therefore, geographical proximity may instead be a better predictor of evolutionary relationship than morphology, especially since gonopodal anatomy is extremely divergent and similarities may be masked by evolutionary convergence. Here we provide a phylogenetics-based test of the power of morphological versus geographical character sets for resolving phylogenetic relationships in xystodesmid millipedes. Molecular data from 90 species-group taxa in the family were included in a six-gene phylogenetic analysis to provide the basis for comparing trees generated from these alternative character sets. The molecular phylogeny was compared to topologies representing three hypotheses: (1) a prior classification formulated using morphological and geographical data, (2) hierarchical groupings derived from Euclidean geographical distance, and (3) one based solely on morphological data. Euclidean geographical distance was not found to be a better predictor of evolutionary relationship than the prior classification, the latter of which was the most similar to the molecular topology. However, all three of the alternative topologies were highly divergent (Bayes factor >10) from the molecular topology, with the tree inferred exclusively from morphology being the most divergent. The results of this analysis show that a high degree of morphological convergence from substantial gonopod shape divergence generated spurious phylogenetic relationships. These results indicate the impact that a high degree of morphological homoplasy may have had on prior treatments of the family. Using the results of our phylogenetic analysis, we make several changes to the classification of the family, including transferring the rare state-threatened speciesSigmoria whiteheadiShelley, 1986 to the genusApheloriaChamberlin, 1921—a relationship not readily apparent based on morphology alone. We show that while gonopod differences are a premier source of taxonomic characters to diagnose species pairwise, the traits should be viewed critically as taxonomic features uniting higher levels.

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Chlamydia trachomatis Tarp Harbors Distinct G and F Actin Binding Domains That Bundle Actin Filaments

Journal of Bacteriology ◽

10.1128/jb.01768-12 ◽

2012 ◽

Vol 195 (4) ◽

pp. 708-716 ◽

Cited By ~ 30

Author(s):

S. Jiwani ◽

S. Alvarado ◽

R. J. Ohr ◽

A. Romero ◽

B. Nguyen ◽

...

Keyword(s):

Chlamydia Trachomatis ◽

Actin Filaments ◽

Actin Binding ◽

Binding Domains

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Prevalence of urogenital, anal, and pharyngeal infections with Chlamydia trachomatis, Neisseria gonorrhoeae, and Mycoplasma genitalium: a cross-sectional study in Reunion island

BMC Infectious Diseases ◽

10.1186/s12879-021-05801-9 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

A. Calas ◽

N. Zemali ◽

G. Camuset ◽

J. Jaubert ◽

R. Manaquin ◽

...

Keyword(s):

Chlamydia Trachomatis ◽

Neisseria Gonorrhoeae ◽

Mycoplasma Genitalium ◽

Cross Sectional Study ◽

Sectional Study ◽

Transmitted Infection ◽

Cross Sectional ◽

Sexually Transmitted ◽

Urogenital Infection ◽

High Prevalence

Abstract Background Recommendations for sexually transmitted infection (STI) screening vary significantly across countries. This study evaluated the prevalence of urogenital and extragenital infections with Chlamydia trachomatis (CT), Neisseria gonorrhoeae (NG), and Mycoplasma genitalium (MG) in patients visiting a French STI clinic in the Indian Ocean region to determine whether current STI screening practices should be updated. Methods This cross-sectional study examined all patients who visited the STI clinic between 2014 and 2015. Triplex polymerase chain reaction screening for CT, NG, and MG was performed on urine, vaginal, pharyngeal, and anal specimens (FTD Urethritis Basic Kit, Fast Track Diagnostics, Luxembourg). Results Of the 851 patients enrolled in the study, 367 were women (367/851, 43.2%) and 484 were men (484/851, 56.0%). Overall, 826 urogenital specimens (826/851, 97.1%), 606 pharyngeal specimens (606/851, 71.2%), and 127 anal specimens (127/851, 14.9%) were taken from enrolled patients. The prevalence of urogenital CT and MG was high in women ≤25 years (19/186, 10.21%; 5/186, 2.69%) and in men who have sex with women ≤30 years (16/212, 7.54%; 5/212, 2.36%). Among patients with urogenital CT infection, 13.7% (7/51) had urethritis. All patients with urogenital MG infection were asymptomatic. Men who have sex with men had a high prevalence of pharyngeal CT (2/45, 4.44%) and NG (3/44, 6.81%) and a high prevalence of anal CT (2/27, 7.41%), NG (2/27, 7.40%), and MG (1/27, 3.70%). After excluding patients with concomitant urogenital infection, extragenital infections with at least 1 of the 3 pathogens were found in 20 swabs (20/91, 21.9%) taken from 16 patients (16/81, 19.7%), all of them asymptomatic. Conclusions Routine multisite screening for CT, NG, and MG should be performed to mitigate the transmission of STIs in high-risk sexually active populations.

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A Comprehensive Phylogenetic and Bioinformatics Survey of Lectins in the Fungal Kingdom

Journal of Fungi ◽

10.3390/jof7060453 ◽

2021 ◽

Vol 7 (6) ◽

pp. 453

Author(s):

Annie Lebreton ◽

François Bonnardel ◽

Yu-Cheng Dai ◽

Anne Imberty ◽

Francis M. Martin ◽

...

Keyword(s):

Evolutionary Relationship ◽

Large Family ◽

Gene Families ◽

Carbohydrate Binding ◽

Sequence Motifs ◽

Fungal Lectin ◽

Quaternary Structures ◽

High Degree ◽

Carbohydrate Ligand ◽

Fungal Kingdom

Fungal lectins are a large family of carbohydrate-binding proteins with no enzymatic activity. They play fundamental biological roles in the interactions of fungi with their environment and are found in many different species across the fungal kingdom. In particular, their contribution to defense against feeders has been emphasized, and when secreted, lectins may be involved in the recognition of bacteria, fungal competitors and specific host plants. Carbohydrate specificities and quaternary structures vary widely, but evidence for an evolutionary relationship within the different classes of fungal lectins is supported by a high degree of amino acid sequence identity. The UniLectin3D database contains 194 fungal lectin 3D structures, of which 129 are characterized with a carbohydrate ligand. Using the UniLectin3D lectin classification system, 109 lectin sequence motifs were defined to screen 1223 species deposited in the genomic portal MycoCosm of the Joint Genome Institute. The resulting 33,485 putative lectin sequences are organized in MycoLec, a publicly available and searchable database. These results shed light on the evolution of the lectin gene families in fungi.

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Isolation and properties of two actin-binding domains in gelsolin.

Journal of Biological Chemistry ◽

10.1016/s0021-9258(18)95726-1 ◽

1985 ◽

Vol 260 (28) ◽

pp. 15232-15238 ◽

Cited By ~ 2

Author(s):

D J Kwiatkowski ◽

P A Janmey ◽

J E Mole ◽

H L Yin

Keyword(s):

Actin Binding ◽

Binding Domains

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Clinical isolates of Tritrichomonas foetus in bulls in Wyoming, South Dakota and Montana, USA

BMC Veterinary Research ◽

10.1186/s12917-020-2229-6 ◽

2020 ◽

Vol 16 (1) ◽

Author(s):

Yinzhu Jin ◽

Aifang Du ◽

Chaoqun Yao

Keyword(s):

Phylogenetic Analysis ◽

South Dakota ◽

United States Of America ◽

The United States ◽

Domestic Cat ◽

Clinical Isolates ◽

Rrna Genes ◽

Tritrichomonas Foetus ◽

Sexually Transmitted ◽

Geographic Regions

Abstract Background Several Tritrichomonas species have been found in mammalian hosts. Among these trichomonads T. foetus is often found in the urogenital tract of cattle and the gastrointestinal tract of the domestic cat, resulting in sexually transmitted bovine trichomonosis and fecal-orally transmitted feline trichomonosis, respectively. The aims of the current study were to molecularly characterize clinical isolates of T. foetus in cattle populations in Wyoming, South Dakota, and Montana of the United States of America and to phylogenetically analyze Tritrichomonas species of mammalian hosts. Results DNA sequencing of rRNA genes showed over 99% identity of the newly described isolates to other bovine isolates. Further, T. foetus isolates of various mammalian hosts originated in different geographic regions worldwide were clustered into two well-defined clades by phylogenetic analysis of rRNA and cysteine protease 2 genes. Clade I consisted of isolates originated from cattle, pig, and human whereas clade II contained isolates of cat and dog. Conclusion It is concluded that all mammalian Tritrichomonas spp. apparently belong to T. foetus. Analysis of more sequences is warranted to support this conclusion.

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