scholarly journals The Mastigamoeba balamuthi Genome and the Nature of the Free-Living Ancestor of Entamoeba

2021 ◽  
Author(s):  
Vojtěch Žárský ◽  
Vladimír Klimeš ◽  
Jan Pačes ◽  
Čestmír Vlček ◽  
Miluše Hradilová ◽  
...  
Keyword(s):  
Surface Membrane ◽  
Structural Features ◽  
Phylogenomic Analysis ◽  
Free Living ◽  
Anaerobic Energy ◽  
Genes Encoding ◽  
Parasitic Lifestyle ◽  
Intestinal Pathogen ◽  
Living Organisms ◽  
Host Parasite

Abstract The transition of free-living organisms to parasitic organisms is a mysterious process that occurs in all major eukaryotic lineages. Parasites display seemingly unique features associated with their pathogenicity; however, it is important to distinguish ancestral preconditions to parasitism from truly new parasite-specific functions. Here, we sequenced the genome and transcriptome of anaerobic free-living Mastigamoeba balamuthi and performed phylogenomic analysis of four related members of the Archamoebae, including Entamoeba histolytica, an important intestinal pathogen of humans. We aimed to trace gene histories throughout the adaptation of the aerobic ancestor of Archamoebae to anaerobiosis and throughout the transition from a free-living to a parasitic lifestyle. These events were associated with massive gene losses that, in parasitic lineages, resulted in a reduction in structural features, complete losses of some metabolic pathways, and a reduction in metabolic complexity. By reconstructing the features of the common ancestor of Archamoebae, we estimated preconditions for the evolution of parasitism in this lineage. The ancestor could apparently form chitinous cysts, possessed proteolytic enzyme machinery, compartmentalized the sulfate activation pathway in mitochondrion-related organelles, and possessed the components for anaerobic energy metabolism. After the split of Entamoebidae, this lineage gained genes encoding surface membrane proteins that are involved in host–parasite interactions. In contrast, gene gains identified in the M. balamuthi lineage were predominantly associated with polysaccharide catabolic processes. A phylogenetic analysis of acquired genes suggested an essential role of lateral gene transfer in parasite evolution (Entamoeba) and in adaptation to anaerobic aquatic sediments (Mastigamoeba).

scholarly journals Symbiotic Adaptation Drives Genome Streamlining of the Cyanobacterial Sponge Symbiont “Candidatus Synechococcus spongiarum”

mBio ◽  
2014 ◽  
Vol 5 (2) ◽  
Author(s):  
Zhao-Ming Gao ◽  
Yong Wang ◽  
Ren-Mao Tian ◽  
Yue Him Wong ◽  
Zenon B. Batang ◽  
...  
Keyword(s):  
Draft Genome ◽  
Evolutionary Relationship ◽  
Extracellular Polysaccharides ◽  
Phylogenomic Analysis ◽  
Free Living ◽  
Repair Enzymes ◽  
Genetic Modifications ◽  
Genes Encoding ◽  
Functional Features ◽  
Genome Level

ABSTRACT“CandidatusSynechococcus spongiarum” is a cyanobacterial symbiont widely distributed in sponges, but its functions at the genome level remain unknown. Here, we obtained the draft genome (1.66 Mbp, 90% estimated genome recovery) of “Ca.Synechococcus spongiarum” strain SH4 inhabiting the Red Sea spongeCarteriospongia foliascens. Phylogenomic analysis revealed a high dissimilarity between SH4 and free-living cyanobacterial strains. Essential functions, such as photosynthesis, the citric acid cycle, and DNA replication, were detected in SH4. Eukaryoticlike domains that play important roles in sponge-symbiont interactions were identified exclusively in the symbiont. However, SH4 could not biosynthesize methionine and polyamines and had lost partial genes encoding low-molecular-weight peptides of the photosynthesis complex, antioxidant enzymes, DNA repair enzymes, and proteins involved in resistance to environmental toxins and in biosynthesis of capsular and extracellular polysaccharides. These genetic modifications imply that “Ca.Synechococcus spongiarum” SH4 represents a low-light-adapted cyanobacterial symbiont and has undergone genome streamlining to adapt to the sponge’s mild intercellular environment.IMPORTANCEAlthough the diversity of sponge-associated microbes has been widely studied, genome-level research on sponge symbionts and their symbiotic mechanisms is rare because they are unculturable. “CandidatusSynechococcus spongiarum” is a widely distributed uncultivated cyanobacterial sponge symbiont. The genome of this symbiont will help to characterize its evolutionary relationship and functional dissimilarity to closely related free-living cyanobacterial strains. Knowledge of its adaptive mechanism to the sponge host also depends on the genome-level research. The data presented here provided an alternative strategy to obtain the draft genome of “Ca.Synechococcus spongiarum” strain SH4 and provide insight into its evolutionary and functional features.

scholarly journals Genome evolution of a non-parasitic secondary heterotroph, the diatom Nitzschia putrida

2021 ◽  
Author(s):  
Ryoma Kamikawa ◽  
Takako Mochizuki ◽  
Mika Sakamoto ◽  
Yasuhiro Tanizawa ◽  
Takuro Nakayama ◽  
...  
Keyword(s):  
Cell Wall ◽  
Gene Families ◽  
Free Living ◽  
Evolutionary Consequence ◽  
Rapid Divergence ◽  
Parasitic Lifestyle ◽  
Living Organisms ◽  
Conserved Gene ◽  
Almost All ◽  
Horizontal Acquisition

AbstractSecondary loss of photosynthesis is observed across almost all plastid-bearing branches of the eukaryotic tree of life. However, genome-based insights into the transition from a phototroph into a secondary heterotroph have so far only been revealed for parasitic species. Free-living organisms can yield unique insights into the evolutionary consequence of the loss of photosynthesis, as the parasitic lifestyle requires specific adaptations to host environments. Here we report on the diploid genome of the free-living diatom Nitzschia putrida (35 Mbp), a non-photosynthetic osmotroph whose photosynthetic relatives contribute ca. 40% of net oceanic primary production. Comparative analyses with photosynthetic diatoms revealed that a combination of genes loss, the horizontal acquisition of genes involved in organic carbon degradation, a unique secretome and the rapid divergence of conserved gene families involved in cell wall and extracellular metabolism appear to have facilitated the lifestyle of a non-parasitic, free-living secondary heterotroph.

scholarly journals Comparative selenoproteome analysis reveals a reduced utilization of selenium in parasitic platyhelminthes

2013 ◽  
Author(s):  
Liang Jiang ◽  
Huazhang Zhu ◽  
Yinzhen Xu ◽  
Jiazuan Ni ◽  
Yan Zhang ◽  
...  
Keyword(s):  
Essential Role ◽  
Evolutionary Dynamics ◽  
Taenia Solium ◽  
Prediction Algorithm ◽  
Free Living ◽  
Important Group ◽  
Parasitic Lifestyle ◽  
Selenoprotein Genes ◽  
Living Organisms ◽  
Almost All

Background: The selenocysteine(Sec)-containing proteins, selenoproteins, are an important group of proteins present in all three kingdoms of life. Although the selenoproteomes of many organisms have been analyzed, systematic studies on selenoproteins in platyhelminthes are still lacking. Moreover, comparison of selenoproteomes between free-living and parasitic animals is rarely studied. Results: In this study, three representative organisms (Schmidtea mediterranea, Schistosoma japonicum and Taenia solium) were selected for comparative analysis of selenoproteomes in Platyhelminthes. Using a SelGenAmic-based selenoprotein prediction algorithm, a total of 37 selenoprotein genes were identified in these organisms. The size of selenoproteomes and selenoprotein families were found to be associated with different lifestyles: free-living organisms have larger selenoproteome whereas parasitic lifestyle corresponds to reduced selenoproteomes. Five selenoproteins, SelT, Sel15, GPx, SPS2 and TR, were found to be present in all examined platyhelminthes as well as almost all sequenced animals, suggesting their essential role in metazoans. Finally, a new splicing form of SelW that lacked the first exon was found to be present in S. japonicum. Conclusions: Our data provide a first glance into the selenoproteomes of organisms in the phylum Platyhelminthes and may help understand function and evolutionary dynamics of selenium utilization in diversified metazoans.

scholarly journals Comparative selenoproteome analysis reveals a reduced utilization of selenium in parasitic platyhelminthes

2013 ◽  
Author(s):  
Liang Jiang ◽  
Huazhang Zhu ◽  
Yinzhen Xu ◽  
Jiazuan Ni ◽  
Yan Zhang ◽  
...  
Keyword(s):  
Essential Role ◽  
Evolutionary Dynamics ◽  
Taenia Solium ◽  
Prediction Algorithm ◽  
Free Living ◽  
Important Group ◽  
Parasitic Lifestyle ◽  
Selenoprotein Genes ◽  
Living Organisms ◽  
Almost All

Background: The selenocysteine(Sec)-containing proteins, selenoproteins, are an important group of proteins present in all three kingdoms of life. Although the selenoproteomes of many organisms have been analyzed, systematic studies on selenoproteins in platyhelminthes are still lacking. Moreover, comparison of selenoproteomes between free-living and parasitic animals is rarely studied. Results: In this study, three representative organisms (Schmidtea mediterranea, Schistosoma japonicum and Taenia solium) were selected for comparative analysis of selenoproteomes in Platyhelminthes. Using a SelGenAmic-based selenoprotein prediction algorithm, a total of 37 selenoprotein genes were identified in these organisms. The size of selenoproteomes and selenoprotein families were found to be associated with different lifestyles: free-living organisms have larger selenoproteome whereas parasitic lifestyle corresponds to reduced selenoproteomes. Five selenoproteins, SelT, Sel15, GPx, SPS2 and TR, were found to be present in all examined platyhelminthes as well as almost all sequenced animals, suggesting their essential role in metazoans. Finally, a new splicing form of SelW that lacked the first exon was found to be present in S. japonicum. Conclusions: Our data provide a first glance into the selenoproteomes of organisms in the phylum Platyhelminthes and may help understand function and evolutionary dynamics of selenium utilization in diversified metazoans.

scholarly journals The assembled and annotated genome of the pigeon louse Columbicola columbae, a model ectoparasite

2021 ◽  
Vol 11 (2) ◽  
Author(s):  
James G Baldwin-Brown ◽  
Scott M Villa ◽  
Anna I Vickrey ◽  
Kevin P Johnson ◽  
Sarah E Bush ◽  
...  
Keyword(s):  
Low Cost ◽  
Single Copy ◽  
Odorant Receptors ◽  
Rna Seq ◽  
Pediculus Humanus ◽  
Final Assembly ◽  
Oxford Nanopore ◽  
Genes Encoding ◽  
Host Parasite ◽  
G Protein Coupled

Abstract The pigeon louse Columbicola columbae is a longstanding and important model for studies of ectoparasitism and host-parasite coevolution. However, a deeper understanding of its evolution and capacity for rapid adaptation is limited by a lack of genomic resources. Here, we present a high-quality draft assembly of the C. columbae genome, produced using a combination of Oxford Nanopore, Illumina, and Hi-C technologies. The final assembly is 208 Mb in length, with 12 chromosome-size scaffolds representing 98.1% of the assembly. For gene model prediction, we used a novel clustering method (wavy_choose) for Oxford Nanopore RNA-seq reads to feed into the MAKER annotation pipeline. High recovery of conserved single-copy orthologs (BUSCOs) suggests that our assembly and annotation are both highly complete and highly accurate. Consistent with the results of the only other assembled louse genome, Pediculus humanus, we find that C. columbae has a relatively low density of repetitive elements, the majority of which are DNA transposons. Also similar to P. humanus, we find a reduced number of genes encoding opsins, G protein-coupled receptors, odorant receptors, insulin signaling pathway components, and detoxification proteins in the C. columbae genome, relative to other insects. We propose that such losses might characterize the genomes of obligate, permanent ectoparasites with predictable habitats, limited foraging complexity, and simple dietary regimes. The sequencing and analysis for this genome were relatively low cost, and took advantage of a new clustering technique for Oxford Nanopore RNAseq reads that will be useful to future genome projects.

scholarly journals Cysteine-Free Proteins in the Immunobiology of Arthropod-Borne Diseases

2010 ◽  
Vol 2010 ◽  
pp. 1-10 ◽  
Author(s):  
J. Santiago Mejia ◽  
Erik N. Arthun ◽  
Richard G. Titus
Keyword(s):  
Plasmodium Falciparum ◽  
Amino Acid ◽  
Distribution Patterns ◽  
Structural Features ◽  
Structure And Function ◽  
Cysteine Residues ◽  
Distribution Analysis ◽  
And Function ◽  
Abundance And Distribution ◽  
Host Parasite

One approach to identify epitopes that could be used in the design of vaccines to control several arthropod-borne diseases simultaneously is to look for common structural features in the secretome of the pathogens that cause them. Using a novel bioinformatics technique, cysteine-abundance and distribution analysis, we found that many different proteins secreted by several arthropod-borne pathogens, includingPlasmodium falciparum, Borrelia burgdorferi, and eight species of Proteobacteria, are devoid of cysteine residues. The identification of three cysteine-abundance and distribution patterns in several families of proteins secreted by pathogenic and nonpathogenic Proteobacteria, and not found when the amino acid analyzed was tryptophan, provides evidence of forces restricting the content of cysteine residues in microbial proteins during evolution. We discuss these findings in the context of protein structure and function, antigenicity and immunogenicity, and host-parasite relationships.

The Poor Osteoinductive Capability of Human Acellular Bone Matrix

2012 ◽  
Vol 35 (12) ◽  
pp. 1061-1069 ◽  
Author(s):  
Yi-Zhou Huang ◽  
Jia-Qin Cai ◽  
Jing Xue ◽  
Xiao-He Chen ◽  
Chao-Liang Zhang ◽  
...  
Keyword(s):  
Bone Regeneration ◽  
Demineralized Bone Matrix ◽  
Bone Matrix ◽  
Structural Features ◽  
Nodule Formation ◽  
Porous Network ◽  
Native Bone ◽  
Genes Encoding ◽  
Osteoid Formation ◽  
Stem Cell Niches

Demineralized bone matrix (DBM) has extensive clinical use for bone regeneration because of its osteoinductive and osteoconductive aptitude. It is suggested that the demineralization process in bone matrix preparation is influential in maintaining osteoinductivity; however, relevant investigations, especially into the osteoinductivity of acellular bone matrix, are not often performed. This study addressed the osteoinductive capability of human acellular cancellous bone matrix (ACBM) after subcutaneous implantation in a rat model. The growth and osteogenic differentiation of rat bone marrow-derived mesenchymal stem cells (rBM-MSCs) seeded in this material were also studied. Without the demineralization process, the ACBM we obtained had an interconnected porous network and the micropores in the surface were clearly exposed. After the ACBM was subcutaneously implanted for 4 months, new osteoid formation was noted but not typical mature bone formation. rBM-MSCs grew well in the ACBM and kept a steady morphology after continuous culture for 28 days. However, no mineralized nodule formation was detected and the expression levels of genes encoding osteogenic markers were significantly decreased. These results demonstrated that human ACBM possess the structural features of native bone and poor osteoinductivity; nonetheless this material helped to preserve the undifferentiated phenotype of rBM-MSCs. Such insights may further broaden our understanding of the application of ACBM for bone regeneration and the creation of stem cell niches.

The possible role of the frontal and sub-parietal gland systems of the pentastomidReighardia sternae(Diesing, 1864) in the evasion of the host immune response

Parasitology ◽  
1979 ◽  
Vol 78 (1) ◽  
pp. 53-66 ◽  
Author(s):  
J. Riley ◽  
J. L. James ◽  
A. A. Banaja
Keyword(s):  
Immune Response ◽  
Alternative Explanation ◽  
Surface Membrane ◽  
Membrane System ◽  
Host Immune Response ◽  
Entire Surface ◽  
Strong Immune Response ◽  
Concomitant Immunity ◽  
Host Parasite

SUMMARYThe frontal and sub-parietal glands of the pentastomidReighardia sternaeelaborate lamellate secretion which is poured on to the cuticle. The entire surface of the cuticle, including the mouth, hook pits and reproductive apertures, is coated with secretion. Electron microscope studies indicate that the glands are continuously active, which implies a turnover of surface membranes. The postulated function of these membranes is to protect certain vital areas of the host–parasite interface, notably the pores of ion-transporting cells, from the host immune response. The available evidence suggests that pentastomids do evoke a strong immune response but since most are long-lived they must circumvent it. We believe the surface membrane system to be instrumental in this. Studies on another pentastomid,Porocephalus crotaliin rats have shown that an immune response stimulated by a primary infection will kill subsequent infections and that the surface membranes are strongly immunogenic. Obvious parallels between this situation and that of schistosome infections in mammals are discussed. An alternative explanation of concomitant immunity is proposed.

scholarly journals Genome Sequence of the Polysaccharide-Degrading, Thermophilic Anaerobe Spirochaeta thermophila DSM 6192

2010 ◽  
Vol 192 (24) ◽  
pp. 6492-6493 ◽  
Author(s):  
Angel Angelov ◽  
Susanne Liebl ◽  
Meike Ballschmiter ◽  
Mechthild Bömeke ◽  
Rüdiger Lehmann ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Glycoside Hydrolase ◽  
Enzyme System ◽  
Cellulose Degradation ◽  
Carbohydrate Binding ◽  
Carbohydrate Binding Module ◽  
Free Living ◽  
Genome Data ◽  
Genes Encoding

ABSTRACT Spirochaeta thermophila is a thermophilic, free-living anaerobe that is able to degrade various α- and β-linked sugar polymers, including cellulose. We report here the complete genome sequence of S. thermophila DSM 6192, which is the first genome sequence of a thermophilic, free-living member of the Spirochaetes phylum. The genome data reveal a high density of genes encoding enzymes from more than 30 glycoside hydrolase families, a noncellulosomal enzyme system for (hemi)cellulose degradation, and indicate the presence of a novel carbohydrate-binding module.

scholarly journals Schistosoma mansonicercariae experience influx of macromolecules during skin penetration

Parasitology ◽  
2009 ◽  
Vol 136 (11) ◽  
pp. 1257-1267 ◽  
Author(s):  
J. THORNHILL ◽  
P. M. Z. COELHO ◽  
P. McVEIGH ◽  
A. MAULE ◽  
A. D. JURBERG ◽  
...  
Keyword(s):  
Molecular Weight ◽  
Lucifer Yellow ◽  
Surface Membrane ◽  
Skin Penetration ◽  
Pharyngeal Muscle ◽  
Novel Host ◽  
Host Parasite ◽  
Fluorescent Molecules ◽  
Germinal Mass

SUMMARYWe have observed that when cercariae penetrate the skin of mice, there is influx into their tissues of Lucifer Yellow and certain labelled molecules of up to 20 kDa molecular weight. This observation was made using a variety of fluorescent membrane-impermeant compounds injected into the skin before the application of cercariae. This unexpected phenomenon was investigated further by transforming cercariaein vitroin the presence of the membrane-impermeant compounds and examining the distribution by microscopy. In schistosomula derived from this procedure, the nephridiopore and surface membrane were labelled while the pre- and post-acetabular glands were not labelled. The region associated with the oesophagus within the pharyngeal muscle clearly contained the fluorescent molecules, as did the region adjacent to the excretory tubules and the germinal mass. We used cercariae stained with carmine to aid identification of regions labelled with Lucifer Yellow. Although the mechanism of this influx is unclear, the observation is significant. From it, we can suggest an hypothesis that, during skin penetration, exposure of internal tissues of the parasite to external macromolecules represents a novel host-parasite interface.

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