scholarly journals Functional Genomics in Caenorhabditis elegans: An Approach Involving Comparisons of Sequences from Related Nematodes

1999 ◽  
Vol 9 (4) ◽  
pp. 348-359 ◽  
Author(s):  
Colin Thacker ◽  
Marco A. Marra ◽  
Alana Jones ◽  
David L. Baillie ◽  
Ann M. Rose
Keyword(s):  
Recombinant Dna ◽  
Genomic Sequence ◽  
Genomic Analysis ◽  
Regulatory Elements ◽  
Pcr Analysis ◽  
Comparative Genomic ◽  
Gene Encoding ◽  
Sequence Comparisons ◽  
C Elegans ◽  
Functional Conservation

Comparative genomic analysis was used to investigate the gene structure of the bli-4 locus from two relatedCaenorhabditis species, C. elegans and C. briggsae. In C. elegans, bli-4 is a complex gene encoding a member of the kex2/subtilisin-like family of proprotein convertases. Genomic sequence comparisons coupled with RT–PCR analysis identified five additional coding exons that had not been identified previously using standard recombinant DNA techniques. The C. briggsae gene was able to rescue both viable blistered and developmentally arrested mutants of C. elegans bli-4, demonstrating functional conservation. In addition, deletion analysis of conserved sequences outside of coding regions, combined with phenotypic rescue experiments, identified regulatory elements that alter the expression of the bli-4 gene. These results demonstrate the utility of genomic sequence comparisons of homologous genes in related species as an effective tool with which to dissect the functional information of complex genes.[The sequence for cosmid K0410 is available at GenBank (accession no. AFO 39719); fosmids G06P23 and G25K01 are available as online supplementary material atwww.genome.org.]

scholarly journals Normocyte-binding protein required for human erythrocyte invasion by the zoonotic malaria parasite Plasmodium knowlesi

2016 ◽  
Vol 113 (26) ◽  
pp. 7231-7236 ◽  
Author(s):  
Robert W. Moon ◽  
Hazem Sharaf ◽  
Claire H. Hastings ◽  
Yung Shwen Ho ◽  
Mridul B. Nair ◽  
...  
Keyword(s):  
Vaccine Development ◽  
Plasmodium Knowlesi ◽  
Binding Protein ◽  
Cynomolgus Macaque ◽  
Genomic Analysis ◽  
Human Infection ◽  
Comparative Genomic ◽  
Gene Encoding ◽  
Human Rbcs

The dominant cause of malaria in Malaysia is now Plasmodium knowlesi, a zoonotic parasite of cynomolgus macaque monkeys found throughout South East Asia. Comparative genomic analysis of parasites adapted to in vitro growth in either cynomolgus or human RBCs identified a genomic deletion that includes the gene encoding normocyte-binding protein Xa (NBPXa) in parasites growing in cynomolgus RBCs but not in human RBCs. Experimental deletion of the NBPXa gene in parasites adapted to growth in human RBCs (which retain the ability to grow in cynomolgus RBCs) restricted them to cynomolgus RBCs, demonstrating that this gene is selectively required for parasite multiplication and growth in human RBCs. NBPXa-null parasites could bind to human RBCs, but invasion of these cells was severely impaired. Therefore, NBPXa is identified as a key mediator of P. knowlesi human infection and may be a target for vaccine development against this emerging pathogen.

scholarly journals Characterization of two atypical promoters and alternate mRNA processing in the mouse Thy-1.2 glycoprotein gene.

1986 ◽  
Vol 6 (8) ◽  
pp. 2923-2931 ◽  
Author(s):  
H A Ingraham ◽  
G A Evans
Keyword(s):  
Genomic Sequence ◽  
Regulatory Elements ◽  
Initiation Site ◽  
Lymphoid Cells ◽  
Gene Encoding ◽  
Specific Expression ◽  
Transcriptional Initiation ◽  
Glycoprotein Gene ◽  
Cell Type Specific Expression ◽  
Flanking Region

The promoter and 5' flanking region of the mouse Thy-1.2 glycoprotein gene were characterized by DNA sequencing, primer extension analysis, and deletion analysis. Transcriptional initiation sites were identified which corresponded to two separate exons upstream of the portion of the gene encoding the Thy-1.2 glycoprotein. We demonstrated that the mouse Thy-1.2 gene was transcribed from two atypical promoters separated by 260 base pairs in the genomic sequence. These promoters contained neither TATAAG nor GGPyCCAATCT homologous sequences but defined a conserved nonamer CTCCCTGCT at -48 from each initiation site. Two Thy-1.2 mRNA species of 1,835 and 1,939 nucleotides, differing in the 5' untranslated region of the mRNA, were thus transcribed from the single Thy-1.2 gene by mRNA splicing to the same downstream exon. Recombinant genomes in which the bacterial chloramphenicol acetyltransferase gene was expressed from either of the two Thy-1.2 promoters demonstrated that each promoter functioned independently and did not direct cell-specific expression in lymphoid cells. The 5' flanking region of the Thy-1.2 gene upstream of -68 could be eliminated without altering cell-type-specific expression. This suggests that regulatory elements responsible for tissue and developmental stage-specific expression of the Thy-1.2 gene are not present in the 5' flanking DNA but may reside downstream of the promoters.

Transcriptional Regulation of the SCL Locus: Identification of an Enhancer That Targets Primitive Erythroid Cells.

Blood ◽  
2004 ◽  
Vol 104 (11) ◽  
pp. 1599-1599
Author(s):  
Eric Delabesse* ◽  
Sarah Ogilvy* ◽  
Michael A. Chapman ◽  
Berthold Göttgens ◽  
Anthony R. Green
Keyword(s):  
Transcriptional Regulation ◽  
T Cell ◽  
Genomic Sequence ◽  
Fetal Liver ◽  
Current Evidence ◽  
Cell Leukaemia ◽  
Bhlh Protein ◽  
Comparative Genomic ◽  
Sequence Comparisons

Abstract The stem cell leukaemia (SCL) gene encodes a bHLH protein that is essential for the formation of all haematopoietic lineages. In addition, maintenance of SCL expression is required for normal differentiation along the erythroid and megakaryocytic lineages, whereas failure to downregulate SCL transcription during T-cell differentiation is associated with T-cell ALL. Current evidence therefore demonstrates that appropriate transcriptional regulation is essential for the biological functions of SCL and this focuses attention on the mechanisms whereby transcription of SCL itself is initiated and maintained. We have previously used biochemical, comparative genomic and transgenic assays to identify 5 distinct enhancers which target different subdomains of the normal SCL expression pattern. However these enhancers do not explain how erythroid expression of SCL is achieved and we have postulated the existence of an additional erythroid enhancer. It is also unclear whether the known SCL enhancers regulate neighbouring genes within the SCL locus. We have therefore quantitated the transcripts from SCL and its neighbouring genes in a large panel of human and murine haematopoietic cell types. Our results reveal a striking and unexpected co-expression of SCL and its downstream neighbour MAP17 (r=0.8; n=31). We demonstrate the existence of appropriately spliced low abundance SCL-MAP17 fusion transcripts suggesting that co-expression reflects transcriptional read-through rather than a shared enhancer. A systematic survey of histone H3 and H4 acetylation throughout the SCL locus was also performed in both cell lines and primary haematopoietic cells. A peak of acetylation downstream of MAP17 (and 40 kb downstream of SCL exon 1a) was found to correlate with expression of SCL but not other neighbouring genes. This region contains peaks of homology in 4-way genomic sequence comparisons (human/dog/mouse/rat) and functions as an erythroid-restricted enhancer in vitro. Morever, in transgenic mice this enhancer directs b-galactosidase expression to the vast majority of circulating primitive erythroblasts but not to fetal liver definitive erythroblasts.

scholarly journals Role of CpSUB1, a Subtilisin-Like Protease, in Cryptosporidium parvum Infection In Vitro

2009 ◽  
Vol 8 (4) ◽  
pp. 470-477 ◽  
Author(s):  
Jane W. Wanyiri ◽  
Patsharaporn Techasintana ◽  
Roberta M. O'Connor ◽  
Michael J. Blackman ◽  
Kami Kim ◽  
...  
Keyword(s):  
Serine Protease ◽  
Cryptosporidium Parvum ◽  
Protease Activity ◽  
Diarrheal Disease ◽  
Genomic Sequence ◽  
Host Cells ◽  
Pcr Analysis ◽  
Apical Region ◽  
Gene Encoding

ABSTRACTThe apicomplexan parasiteCryptosporidiumis a significant cause of diarrheal disease worldwide. Previously, we reported that aCryptosporidium parvumsubtilisin-like serine protease activity with furin-type specificity cleaves gp40/15, a glycoprotein that is proteolytically processed into gp40 and gp15, which are implicated in mediating infection of host cells. Neither the enzyme(s) responsible for the protease activity inC. parvumlysates nor those that process gp40/15 are known. There are no furin or other proprotein convertase genes in theC. parvumgenome. However, a gene encoding CpSUB1, a subtilisin-like serine protease, is present. In this study, we cloned the CpSUB1 genomic sequence and expressed and purified the recombinant prodomain. Reverse transcriptase PCR analysis of RNA fromC. parvum-infected HCT-8 cells revealed that CpSUB1 is expressed throughout infection in vitro. In immunoblots, antiserum to the recombinant CpSUB1 prodomain revealed two major bands, of ∼64 kDa and ∼48 kDa, forC. parvumlysates and proteins “shed” during excystation. In immunofluorescence assays, the antiserum reacted with the apical region of sporozoites and merozoites. The recombinant prodomain inhibited protease activity and processing of recombinant gp40/15 byC. parvumlysates but not by furin. Since prodomains are often selective inhibitors of their cognate enzymes, these results suggest that CpSUB1 may be a likely candidate for the protease activity inC. parvumand for processing of gp40/15. Importantly, the recombinant prodomain inhibitedC. parvuminfection of HCT-8 cells. These studies indicate that CpSUB1 plays a significant role in infection of host cells by the parasite and suggest that this enzyme may serve as a target for intervention.

scholarly journals A Bayesian implementation of the multispecies coalescent model with introgression for comparative genomic analysis

2019 ◽  
Author(s):  
Thomas Flouris ◽  
Xiyun Jiao ◽  
Bruce Rannala ◽  
Ziheng Yang
Keyword(s):  
Gene Flow ◽  
Genomic Sequence ◽  
Sequence Data ◽  
Incomplete Lineage Sorting ◽  
Mosquito Species ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
Lineage Sorting ◽  
Multispecies Coalescent ◽  
Important Means

AbstractRecent analyses suggest that cross-species gene flow or introgression is common in nature, especially during species divergences. Genomic sequence data can be used to infer introgression events and to estimate the timing and intensity of introgression, providing an important means to advance our understanding of the role of gene flow in speciation. Here we implement the multispecies-coalescent-with-introgression (MSci) model, an extension of the multispecies-coalescent (MSC) model to incorporate introgression, in our Bayesian Markov chain Monte Carlo (MCMC) program BPP. The MSci model accommodates deep coalescence (or incomplete lineage sorting) and introgression and provides a natural framework for inference using genomic sequence data. Computer simulation confirms the good statistical properties of the method, although hundreds or thousands of loci are typically needed to estimate introgression probabilities reliably. Re-analysis of datasets from the purple cone spruce confirms the hypothesis of homoploid hybrid speciation. We estimated the introgression probability using the genomic sequence data from six mosquito species in the Anopheles gambiae species complex, which varies considerably across the genome, likely driven by differential selection against introgressed alleles.

scholarly journals Eutherian comparative genomic analysis protocol

2020 ◽  
Author(s):  
Marko Premzl
Keyword(s):  
Genomic Sequence ◽  
Sequence Data ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Third Party ◽  
Comparative Genomic ◽  
Data Sets ◽  
Gene Data ◽  
Sequence Errors ◽  
Analysis Protocol

Abstract The eutherian genomics momentum greatly advanced biology and medicine. Nevertheless, future revisions and updates of eutherian genomic sequence data sets were expected, due to potential genomic sequence errors and incompleteness of genomic sequences. The eutherian comparative genomic analysis protocol was established as guidance in protection against potential genomic sequence errors in public eutherian genomic sequence assemblies. The protocol revised, updated and published 12 major eutherian gene data sets, including 1853 complete coding sequences deposited in European Nucleotide Archive as curated third party data gene data sets under accession numbers: FR734011-FR734074, HF564658-HF564785, HF564786-HF564815, HG328835-HG329089, HG426065-HG426183, HG931734-HG931849, LM644135-LM644234, LN874312-LN874522, LT548096-LT548244, LT631550-LT631670, LT962964-LT963174 and LT990249-LT990597.

scholarly journals Pseudomonas donghuensis HYS gtrA/B/II Gene Cluster Contributes to Its Pathogenicity toward Caenorhabditis elegans

2021 ◽  
Vol 22 (19) ◽  
pp. 10741
Author(s):  
Yaqian Xiao ◽  
Panning Wang ◽  
Xuesi Zhu ◽  
Zhixiong Xie
Keyword(s):  
Caenorhabditis Elegans ◽  
Gene Cluster ◽  
Mapk Pathway ◽  
Genomic Analysis ◽  
Virulence Gene ◽  
Comparative Genomic ◽  
Specific Gene ◽  
C Elegans ◽  
O Antigen ◽  
Specific Virulence

Pseudomonas donghuensis HYS is more virulent than P. aeruginosa toward Caenorhabditis elegans but the mechanism underlying virulence is unclear. This study is the first to report that the specific gene cluster gtrA/B/II in P. donghuensis HYS is involved in the virulence of this strain toward C. elegans, and there are no reports of GtrA, GtrB and GtrII in any Pseudomonas species. The pathogenicity of P. donghuensis HYS was evaluated using C. elegans as a host. Based on the prediction of virulence factors and comparative genomic analysis of P. donghuensis HYS, we identified 42 specific virulence genes in P. donghuensis HYS. Slow-killing assays of these genes showed that the gtrAB mutation had the greatest effect on the virulence of P. donghuensis HYS, and GtrA, GtrB and GtrII all positively affected P. donghuensis HYS virulence. Two critical GtrII residues (Glu47 and Lys480) were identified in P. donghuensis HYS. Transmission electron microscopy (TEM) showed that GtrA, GtrB and GtrII were involved in the glucosylation of lipopolysaccharide (LPS) O-antigen in P. donghuensis HYS. Furthermore, colony-forming unit (CFU) assays showed that GtrA, GtrB and GtrII significantly enhanced P. donghuensis HYS colonization in the gut of C. elegans, and glucosylation of LPS O-antigen and colonization in the host intestine contributed to the pathogenicity of P. donghuensis HYS. In addition, experiments using the worm mutants ZD101, KU4 and KU25 revealed a correlation between P. donghuensis HYS virulence and the TIR-1/SEK-1/PMK-1 pathways of the innate immune p38 MAPK pathway in C. elegans. In conclusion, these results reveal that the specific virulence gene cluster gtrA/B/II contributes to the unique pathogenicity of HYS compared with other pathogenic Pseudomonas, and that this process also involves C. elegans innate immunity. These findings significantly increase the available information about GtrA/GtrB/GtrII-based virulence mechanisms in the genus Pseudomonas.

scholarly journals Candidate pathogenicity islands in the genome of ‘CandidatusRickettsiella isopodorum’, an intracellular bacterium infecting terrestrial isopod crustaceans

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2806 ◽  
Author(s):  
YaDong Wang ◽  
Christopher Chandler
Keyword(s):  
Genomic Island ◽  
Genomic Sequence ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic ◽  
Photorhabdus Luminescens ◽  
Future Studies ◽  
Terrestrial Isopod ◽  
Microbe Interactions ◽  
Host Microbe Interactions

The bacterial genusRickettsiellabelongs to the order Legionellales in the Gammaproteobacteria, and consists of several described species and pathotypes, most of which are considered to be intracellular pathogens infecting arthropods. Two members of this genus,R. grylliandR. isopodorum, are known to infect terrestrial isopod crustaceans. In this study, we assembled a draft genomic sequence forR. isopodorum, and performed a comparative genomic analysis withR. grylli. We found evidence for several candidate genomic island regions inR. isopodorum, none of which appear in the previously availableR. grylligenome sequence.Furthermore, one of these genomic island candidates inR. isopodorumcontained a gene that encodes a cytotoxin partially homologous to those found inPhotorhabdus luminescensandXenorhabdus nematophilus(Enterobacteriaceae), suggesting that horizontal gene transfer may have played a role in the evolution of pathogenicity inRickettsiella. These results lay the groundwork for future studies on the mechanisms underlying pathogenesis inR. isopodorum, and this system may provide a good model for studying the evolution of host-microbe interactions in nature.

scholarly journals Eutherian comparative genomic analysis protocol

2019 ◽  
Author(s):  
Marko Premzl
Keyword(s):  
Genomic Sequence ◽  
Sequence Data ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Third Party ◽  
Comparative Genomic ◽  
Data Sets ◽  
Gene Data ◽  
Sequence Errors ◽  
Analysis Protocol

Abstract The eutherian genomics momentum greatly advanced biology and medicine. Nevertheless, future revisions and updates of eutherian genomic sequence data sets were expected, due to potential genomic sequence errors and incompleteness of genomic sequences. The eutherian comparative genomic analysis protocol was established as guidance in protection against potential genomic sequence errors in public eutherian genomic sequence assemblies. The protocol revised, updated and published 11 major eutherian gene data sets, including 1504 complete coding sequences deposited in European Nucleotide Archive as curated third party data gene data sets under accession numbers: FR734011-FR734074, HF564658-HF564785, HF564786-HF564815, HG328835-HG329089, HG426065-HG426183, HG931734-HG931849, LM644135-LM644234, LN874312-LN874522, LT548096-LT548244, LT631550-LT631670 and LT962964-LT963174.

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