scholarly journals Transcriptional signatures of clonally derived Toxoplasma tachyzoites reveal novel insights into the expression of a family of surface proteins.

2021 ◽  
Author(s):  
Terence Charles Theisen ◽  
John C. Boothroyd
Keyword(s):  
Gene Expression ◽  
Immune Response ◽  
Toxoplasma Gondii ◽  
Gene Family ◽  
Gene Families ◽  
Surface Proteins ◽  
Paralogous Gene ◽  
Specific Expression ◽  
Related Sequence ◽  
Warm Blooded Animal

Toxoplasma gondii has numerous, large, paralogous gene families that are likely critical for supporting its unparalleled host range: nearly any nucleated cell in almost any warm-blooded animal. The SRS (SAG1-related sequence) gene family encodes over 100 proteins, the most abundant of which are thought to be involved in parasite attachment and, based on their stage-specific expression, evading the host immune response. For most SRS proteins, however, little is understood about their function and expression profile. Single-parasite RNA-sequencing previously demonstrated that across an entire population of lab-grown tachyzoites, transcripts for over 70 SRS genes were detected in at least one parasite. In any one parasite, however, transcripts for an average of only 7 SRS genes were detected, two of which, SAG1 and SAG2A , were extremely abundant and detected in virtually all. These data do not address whether this pattern of sporadic SRS gene expression is consistently inherited among the progeny of a given parasite or arises independently of lineage. We hypothesized that if SRS expression signatures are stably inherited by progeny, subclones isolated from a cloned parent would be more alike in their expression signatures than they are to the offspring of another clone. In this report, we compare transcriptomes of clonally derived parasites to determine the degree to which expression of the SRS family is stably inherited in individual parasites. Our data indicate that in RH tachyzoites, SRS genes are variably expressed even between parasite samples subcloned from the same parent within approximately 10 parasite divisions (72 hours). This suggests that the pattern of sporadically expressed SRS genes is highly variable and not driven by inheritance mechanisms, at least under our conditions.

scholarly journals Temporal Expression Analysis of the Borrelia burgdorferi Paralogous Gene Family 54 Genes BBA64, BBA65, and BBA66 during Persistent Infection in Mice

2007 ◽  
Vol 75 (6) ◽  
pp. 2753-2764 ◽  
Author(s):  
Robert D. Gilmore ◽  
Rebekah R. Howison ◽  
Virginia L. Schmit ◽  
Andrew J. Nowalk ◽  
Dawn R. Clifton ◽  
...  
Keyword(s):  
Gene Expression ◽  
Borrelia Burgdorferi ◽  
Gene Family ◽  
Expression Profile ◽  
Persistent Infection ◽  
Adaptive Immune Response ◽  
Paralogous Gene ◽  
Reverse Transcription Pcr ◽  
Paralogous Gene Family

ABSTRACT Members of the Borrelia burgdorferi paralogous gene family 54 (pgf 54) are regulated by conditions simulating mammalian infection and are thought to be instrumental in borrelial host survival and pathogenesis. To explore the activities of these genes in vivo, a comprehensive analysis of pgf 54 genes BBA64, BBA65, and BBA66 was performed to assess the genetic stability, host antibody responses, and kinetics of gene expression in the murine model of persistent infection. DNA sequencing of pgf 54 genes obtained from reisolates at 1 year postinfection demonstrated that all genes of this family are stable and do not undergo recombination to generate variant antigens during persistent infection. Antibodies against BBA64 and BBA66 appeared soon after infection and were detectable throughout the infection, suggesting that there was gene expression during infection. However, quantitative reverse transcription-PCR revealed that BBA64 gene expression was considerably decreased in Borrelia residing in the mouse ear tissue compared to the expression in cultured spirochetes by 20 days postinfection and that the levels of expression remained low throughout the infection. Conversely, transcription of the BBA65 and BBA66 genes was increased, and both of these genes were continuously expressed until 100 days postinfection; this was followed by periods of differential expression late in infection. The expression profile of the BBA64 gene suggests that this gene has an important role during tick-to-host transmission and early infection, whereas the expression profile of the BBA65 and BBA66 genes suggests that these genes have a role in persistent infection. The differential regulation of pgf 54 genes observed during infection may help confer a survival advantage during persistent infection, influencing mechanisms for B. burgdorferi dissemination, tissue tropism, or evasion of the adaptive immune response.

scholarly journals Demonstration of the Genetic Stability and Temporal Expression of Select Members of the Lyme Disease Spirochete OspF Protein Family during Infection in Mice

2001 ◽  
Vol 69 (8) ◽  
pp. 4831-4838 ◽  
Author(s):  
John V. McDowell ◽  
Shian Ying Sung ◽  
Gregory Price ◽  
Richard T. Marconi
Keyword(s):  
Immune Response ◽  
Lyme Disease ◽  
Gene Family ◽  
Immune Evasion ◽  
Humoral Immune Response ◽  
Genetic Stability ◽  
Gene Families ◽  
Time Frame ◽  
Protein Family ◽  
Humoral Immune

ABSTRACT Infection with Lyme disease spirochetes can be chronic. This suggests that the spirochetes are capable of immune evasion. In a previous study we demonstrated that the ospE gene family, which is one of three gene families whose members are flanked at their 5′ end by the highly conserved upstream homology box (UHB) element, undergoes mutation and rearrangement during infection. This results in the generation of antigenically distinct variants that may contribute to immune evasion. In this study we have assessed the genetic stability of the UHB-flanked ospF gene family during infection in mice. Using postinfection clonal populations of Borrelia burgdorferi B31MI, PCR amplicons were generated for three members of the ospF gene family after a 3-month infection time frame. The amplicons were analyzed by single-nucleotide polymorphism pattern analysis and DNA sequencing. Members of the ospFgene family were found to be stable during infection, as no mutations or rearrangements were detected. An analysis of the humoral immune response to these proteins during infection revealed that the immune response to each is specific and that there is a delayed humoral immune response to some OspF protein family members. These analyses suggest that there is a temporal component to the expression of these genes during infection. In addition to a possible contribution to immune evasion, members of the OspF protein family may play specific roles at different stages of infection.

scholarly journals Transcription Profiles Associated with Inducible Adhesion in Candida parapsilosis

mSphere ◽  
2021 ◽  
Vol 6 (1) ◽  
Author(s):  
Joseph M. Bliss ◽  
George A. Tollefson ◽  
Abigail Cuevas ◽  
Sarah J. Longley ◽  
Matthew N. Neale ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Family ◽  
Candida Parapsilosis ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Enrichment Analysis ◽  
Gene Families ◽  
Mammalian Host ◽  
Emerging Infections ◽  
Content Type

ABSTRACT Candida parapsilosis has emerged as a frequent cause of invasive candidiasis with increasing evidence of unique biological features relative to C. albicans. As it adapts to conditions within a mammalian host, rapid changes in gene expression are necessary to facilitate colonization and persistence in this environment. Adhesion of the organism to biological surfaces is a key first step in this process and is the focus of this study. Building on previous observations showing the importance of a member of the ALS gene family in C. parapsilosis adhesion, three clinical isolates were cultured under two conditions that mimic the mammalian host and promote adhesion, incubation at 37°C in tissue culture medium 199 or in human plasma. Transcriptional profiles using RNA-seq were obtained in these adhesion-inducing conditions and compared to profiles following growth in yeast media that suppress adhesion to identify gene expression profiles associated with adhesion. Overall gene expression profiles among the three strains were similar in both adhesion-inducing conditions and distinct from adhesion-suppressing conditions. Pairwise analysis among the three growth conditions identified 133 genes that were differentially expressed at a cutoff of ±4-fold, with the most upregulated genes significantly enriched in iron acquisition and transmembrane transport, while the most downregulated genes were enriched in oxidation-reduction processes. Gene family enrichment analysis identified gene families with diverse functions that may have an important role in this important step for colonization and disease. IMPORTANCE Invasive Candida infections are frequent complications of the immunocompromised and are associated with substantive morbidity and mortality. Although C. albicans is the best-studied species, emerging infections by non-albicans Candida species have led to increased efforts to understand aspects of their pathogenesis that are unique from C. albicans. C. parapsilosis is a frequent cause of invasive infections, particularly among premature infants. Recent efforts have identified important virulence mechanisms that have features distinct from C. albicans. C. parapsilosis can exist outside a host environment and therefore requires rapid modifications when it encounters a mammalian host to prevent its clearance. An important first step in the process is adhesion to host surfaces. This work takes a global, nonbiased approach to investigate broad changes in gene expression that accompany efficient adhesion. As such, biological pathways and individual protein targets are identified that may be amenable to manipulation to reduce colonization and disease from this organism.

scholarly journals Murine V kappa gene expression does not follow the VH paradigm.

1989 ◽  
Vol 169 (5) ◽  
pp. 1859-1864 ◽  
Author(s):  
A Kaushik ◽  
D H Schulze ◽  
C Bona ◽  
G Kelsoe
Keyword(s):  
Gene Expression ◽  
Gene Family ◽  
B Lymphocytes ◽  
Gene Rearrangement ◽  
Gene Families ◽  
Genomic Complexity ◽  
Positional Bias ◽  
Vh Gene

V kappa gene family expression among LPS-reactive murine B lymphocytes, unlike that of VH gene families, is not proportional to genomic complexity, i.e., nonstoichiometric. Furthermore, no positional bias for the overexpression of J-proximal V kappa genes (V kappa 21) is observed among neonatal B lymphocytes. Yet, the V kappa 1 and V kappa 9 families located in the center of V kappa locus are preferentially used by neonatal B splenocytes. Thus, the mechanisms of V kappa gene rearrangement and expression appear to differ significantly from those controlling the VH locus.

scholarly journals Toxoplasma gondii Asexual Development: Identification of Developmentally Regulated Genes and Distinct Patterns of Gene Expression

2002 ◽  
Vol 1 (3) ◽  
pp. 329-340 ◽  
Author(s):  
Michael D. Cleary ◽  
Upinder Singh ◽  
Ira J. Blader ◽  
Jeremy L. Brewer ◽  
John C. Boothroyd
Keyword(s):  
Gene Expression ◽  
Toxoplasma Gondii ◽  
Expression Profiles ◽  
Protozoan Parasite ◽  
Transcript Abundance ◽  
Surface Proteins ◽  
Asexual Development ◽  
Mrna Levels ◽  
Developmentally Regulated ◽  
Transcript Levels

ABSTRACT Asexual development in Toxoplasma gondii is a vital aspect of the parasite's life cycle, allowing transmission and avoidance of the host immune response. Differentiation of rapidly dividing tachyzoites into slowly growing, encysted bradyzoites involves significant changes in both physiology and morphology. We generated microarrays of ∼4,400 Toxoplasma cDNAs, representing a minimum of ∼600 genes (based on partial sequencing), and used these microarrays to study changes in transcript levels during tachyzoite-to-bradyzoite differentiation. This approach has allowed us to (i) determine expression profiles of previously described developmentally regulated genes, (ii) identify novel developmentally regulated genes, and (iii) identify distinct classes of genes based on the timing and magnitude of changes in transcript levels. Whereas microarray analysis typically involves comparisons of mRNA levels at different time points, we have developed a method to measure relative transcript abundance between genes at a given time point. This method was used to determine transcript levels in parasites prior to differentiation and to further classify bradyzoite-induced genes, thus allowing a more comprehensive view of changes in gene expression than is provided by standard expression profiles. Newly identified developmentally regulated genes include putative surface proteins (a SAG1-related protein, SRS9, and a mucin-domain containing protein), regulatory and metabolic enzymes (methionine aminopeptidase, oligopeptidase, aminotransferase, and glucose-6-phosphate dehydrogenase homologues), and a subset of genes encoding secretory organelle proteins (MIC1, ROP1, ROP2, ROP4, GRA1, GRA5, and GRA8). This analysis permits the first in-depth look at changes in gene expression during development of this complex protozoan parasite.

scholarly journals Natural transposable element insertions drive expression changes in genes underlying Drosophila immune response

2019 ◽  
Author(s):  
Anna Ullastres ◽  
Miriam Merenciano ◽  
Josefa González
Keyword(s):  
Gene Expression ◽  
Immune Response ◽  
Transposable Element ◽  
Individual Variability ◽  
Gram Negative Bacteria ◽  
Specific Expression ◽  
Allele Specific Expression ◽  
Allele Specific ◽  
Immune Related Genes ◽  
First Time

ABSTRACTVariation in gene expression underlies inter-individual variability in immune response. However, the mutations responsible for gene expression changes remain largely unknown. In this work, we searched for transposable element insertions present at high population frequencies and located nearby immune-related genes in Drosophila melanogaster. We identified 12 insertions associated with allele-specific expression changes in immune-related genes. We showed that transgenically induced expression changes in most of these genes are associated with differences in survival to infection with the gram-negative bacteria Pseudomonas entomophila. We provide experimental evidence suggesting a causal role for five insertions in the allele-specific expression changes observed. Furthermore, for two insertions we found a significant association with increased tolerance to bacterial infection. Our results showed for the first time that polymorphic transposable element insertions from different families drive expression changes in genes that are relevant for inter-individual differences in immune response.

scholarly journals Genome-wide identification, and phylogenetic and expression profiling analyses, of XTH gene families in Brassica rapa L. and Brassica oleracea L.

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Di Wu ◽  
Anqi Liu ◽  
Xiaoyu Qu ◽  
Jiayi Liang ◽  
Min Song
Keyword(s):  
Cell Wall ◽  
Gene Family ◽  
Brassica Oleracea ◽  
Brassica Rapa ◽  
Multigene Family ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Gene Families ◽  
Specific Expression ◽  
Group I

Abstract Background Xyloglucan endotransglucosylase/hydrolase genes (XTHs) are a multigene family and play key roles in regulating cell wall extensibility in plant growth and development. Brassica rapa and Brassica oleracea contain XTHs, but detailed identification and characterization of the XTH family in these species, and analysis of their tissue expression profiles, have not previously been carried out. Results In this study, 53 and 38 XTH genes were identified in B. rapa and B. oleracea respectively, which contained some novel members not observed in previous studies. All XTHs of B. rapa, B. oleracea and Arabidopsis thaliana could be classified into three groups, Group I/II, III and the Early diverging group, based on phylogenetic relationships. Gene structures and motif patterns were similar within each group. All XTHs in this study contained two characteristic conserved domains (Glyco_hydro and XET_C). XTHs are located mainly in the cell wall but some are also located in the cytoplasm. Analyses of the mechanisms of gene family expansion revealed that whole-genome triplication (WGT) events and tandem duplication (TD) may have been the major mechanisms accounting for the expansion of the XTH gene family. Interestingly, TD genes all belonged to Group I/II, suggesting that TD was the main reason for the largest number of genes being in these groups. B. oleracea had lost more of the XTH genes, the conserved domain XET_C and the conserved active-site motif EXDXE compared with B. rapa, consistent with asymmetrical evolution between the two Brassica genomes. A majority of XTH genes exhibited different tissue-specific expression patterns based on RNA-seq data analyses. Moreover, there was differential expression of duplicated XTH genes in the two species, indicating that their functional differentiation occurred after B. rapa and B. oleracea diverged from a common ancestor. Conclusions We carried out the first systematic analysis of XTH gene families in B. rapa and B. oleracea. The results of this investigation can be used for reference in further studies on the functions of XTH genes and the evolution of this multigene family.

scholarly journals Identification and expression profile analysis of the sucrose phosphate synthase gene family in Litchi chinensis Sonn.

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4379 ◽  
Author(s):  
Dan Wang ◽  
Jietang Zhao ◽  
Bing Hu ◽  
Jiaqi Li ◽  
Yaqi Qin ◽  
...  
Keyword(s):  
Gene Family ◽  
Profile Analysis ◽  
Functional Divergence ◽  
Expression Patterns ◽  
Sucrose Phosphate Synthase ◽  
Gene Families ◽  
Specific Expression ◽  
Litchi Chinensis ◽  
Sucrose Phosphate ◽  
Phosphate Synthase

Sucrose phosphate synthase (SPS, EC 2.4.1.14) is a key enzyme that regulates sucrose biosynthesis in plants. SPS is encoded by different gene families which display differential expression patterns and functional divergence. Genome-wide identification and expression analyses of SPS gene families have been performed in Arabidopsis, rice, and sugarcane, but a comprehensive analysis of the SPS gene family in Litchi chinensis Sonn. has not yet been reported. In the current study, four SPS gene (LcSPS1, LcSPS2, LcSPS3, and LcSPS4) were isolated from litchi. The genomic organization analysis indicated the four litchi SPS genes have very similar exon-intron structures. Phylogenetic tree showed LcSPS1-4 were grouped into different SPS families (LcSPS1 and LcSPS2 in A family, LcSPS3 in B family, and LcSPS4 in C family). LcSPS1 and LcSPS4 were strongly expressed in the flowers, while LcSPS3 most expressed in mature leaves. RT-qPCR results showed that LcSPS genes expressed differentially during aril development between cultivars with different hexose/sucrose ratios. A higher level of expression of LcSPS genes was detected in Wuheli, which accumulates higher sucrose in the aril at mature. The tissue- and developmental stage-specific expression of LcSPS1-4 genes uncovered in this study increase our understanding of the important roles played by these genes in litchi fruits.

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