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 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 Atypical Membrane-Anchored Cytokine MIF in a Marine Dinoflagellate

2020 ◽  
Vol 8 (9) ◽  
pp. 1263
Author(s):  
Maëlle Jaouannet ◽  
Anne-Sophie Pavaux ◽  
Sophie Pagnotta ◽  
Olivier Pierre ◽  
Claire Michelet ◽  
...  
Keyword(s):  
Cell Wall ◽  
Extracellular Vesicles ◽  
Transmembrane Protein ◽  
Macrophage Migration ◽  
Phylogenetic Groups ◽  
Free Living ◽  
Immune Systems ◽  
Marine Dinoflagellate ◽  
Living Organisms ◽  
Planktonic Communities

Macrophage Migration Inhibitory Factors (MIF) are pivotal cytokines/chemokines for vertebrate immune systems. MIFs are typically soluble single-domain proteins that are conserved across plant, fungal, protist, and metazoan kingdoms, but their functions have not been determined in most phylogenetic groups. Here, we describe an atypical multidomain MIF protein. The marine dinoflagellate Lingulodinium polyedra produces a transmembrane protein with an extra-cytoplasmic MIF domain, which localizes to cell-wall-associated membranes and vesicular bodies. This protein is also present in the membranes of extracellular vesicles accumulating at the secretory pores of the cells. Upon exposure to biotic stress, L. polyedra exhibits reduced expression of the MIF gene and reduced abundance of the surface-associated protein. The presence of LpMIF in the membranes of secreted extracellular vesicles evokes the fascinating possibility that LpMIF may participate in intercellular communication and/or interactions between free-living organisms in multispecies planktonic communities.

scholarly journals The reference genome and transcriptome of the limestone langur, Trachypithecus leucocephalus, reveal expansion of genes related to alkali tolerance

BMC Biology ◽  
2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Tengcheng Que ◽  
Huifeng Wang ◽  
Weifei Yang ◽  
Jianbao Wu ◽  
Chenyang Hou ◽  
...  
Keyword(s):  
De Novo ◽  
Great Majority ◽  
Gene Families ◽  
Functional Enrichment ◽  
Mineral Absorption ◽  
Iron Storage ◽  
Trachypithecus Leucocephalus ◽  
Karst Environment ◽  
Alkali Tolerance ◽  
Almost All

Abstract Background Trachypithecus leucocephalus, the white-headed langur, is a critically endangered primate that is endemic to the karst mountains in the southern Guangxi province of China. Studying the genomic and transcriptomic mechanisms underlying its local adaptation could help explain its persistence within a highly specialized ecological niche. Results In this study, we used PacBio sequencing and optical assembly and Hi-C analysis to create a high-quality de novo assembly of the T. leucocephalus genome. Annotation and functional enrichment revealed many genes involved in metabolism, transport, and homeostasis, and almost all of the positively selected genes were related to mineral ion binding. The transcriptomes of 12 tissues from three T. leucocephalus individuals showed that the great majority of genes involved in mineral absorption and calcium signaling were expressed, and their gene families were significantly expanded. For example, FTH1 primarily functions in iron storage and had 20 expanded copies. Conclusions These results increase our understanding of the evolution of alkali tolerance and other traits necessary for the persistence of T. leucocephalus within an ecologically unique limestone karst environment.

scholarly journals The Diverse Calpain Family in Trypanosomatidae: Functional Proteins Devoid of Proteolytic Activity?

Cells ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 299
Author(s):  
Vítor Ennes-Vidal ◽  
Marta Helena Branquinha ◽  
André Luis Souza dos Santos ◽  
Claudia Masini d’Avila-Levy
Keyword(s):  
Proteolytic Activity ◽  
Current Knowledge ◽  
Current Therapy ◽  
Calcium Dependent ◽  
Administration Routes ◽  
Life Threatening ◽  
Living Organisms ◽  
Almost All ◽  
Open Question ◽  
Calpain Inhibitors

Calpains are calcium-dependent cysteine peptidases that were originally described in mammals and, thereafter, their homologues were identified in almost all known living organisms. The deregulated activity of these peptidases is associated with several pathologies and, consequently, huge efforts have been made to identify selective inhibitors. Trypanosomatids, responsible for life-threatening human diseases, possess a large and diverse family of calpain sequences in their genomes. Considering that the current therapy to treat trypanosomatid diseases is limited to a handful of drugs that suffer from unacceptable toxicity, tough administration routes, like parenteral, and increasing treatment failures, a repurposed approach with calpain inhibitors could be a shortcut to successful chemotherapy. However, there is a general lack of knowledge about calpain functions in these parasites and, currently, the proteolytic activity of these proteins is still an open question. Here, we highlight the current research and perspectives on trypanosomatid calpains, overview calpain description in these organisms, and explore the potential of targeting the calpain system as a therapeutic strategy. This review gathers the current knowledge about this fascinating family of peptidases as well as insights into the puzzle: are we unable to measure calpain activity in trypanosomatids, or are the functions of these proteins devoid of proteolytic activity in these parasites?

scholarly journals Systematic Detection of Large-Scale Multi-Gene Horizontal Transfer in Prokaryotes

2021 ◽  
Author(s):  
Lina Kloub ◽  
Sean Gosselin ◽  
Matthew Fullmer ◽  
Joerg Graf ◽  
J Peter Gogarten ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Large Scale ◽  
Single Gene ◽  
Gene Families ◽  
Microbial Evolution ◽  
Phylogenetic Distance ◽  
Secretion Systems ◽  
Type Iii Secretion Systems ◽  
A Genome ◽  
Conserved Gene

Abstract Horizontal gene transfer (HGT) is central to prokaryotic evolution. However, little is known about the “scale” of individual HGT events. In this work, we introduce the first computational framework to help answer the following fundamental question: How often does more than one gene get horizontally transferred in a single HGT event? Our method, called HoMer, uses phylogenetic reconciliation to infer single-gene HGT events across a given set of species/strains, employs several techniques to account for inference error and uncertainty, combines that information with gene order information from extant genomes, and uses statistical analysis to identify candidate horizontal multi-gene transfers (HMGTs) in both extant and ancestral species/strains. HoMer is highly scalable and can be easily used to infer HMGTs across hundreds of genomes. We apply HoMer to a genome-scale dataset of over 22000 gene families from 103 Aeromonas genomes and identify a large number of plausible HMGTs of various scales at both small and large phylogenetic distances. Analysis of these HMGTs reveals interesting relationships between gene function, phylogenetic distance, and frequency of multi-gene transfer. Among other insights, we find that (i) the observed relative frequency of HMGT increases as divergence between genomes increases, (ii) HMGTs often have conserved gene functions, and (iii) rare genes are frequently acquired through HMGT. We also analyze in detail HMGTs involving the zonula occludens toxin and type III secretion systems. By enabling the systematic inference of HMGTs on a large scale, HoMer will facilitate a more accurate and more complete understanding of HGT and microbial evolution.

scholarly journals Circadian Deregulation as Possible New Player in Pollution-Induced Tissue Damage

Atmosphere ◽  
2021 ◽  
Vol 12 (1) ◽  
pp. 116
Author(s):  
Mascia Benedusi ◽  
Elena Frigato ◽  
Cristiano Bertolucci ◽  
Giuseppe Valacchi
Keyword(s):  
Cardiovascular Diseases ◽  
Air Pollutants ◽  
Environmental Stressors ◽  
Common Mechanism ◽  
Particulate Matters ◽  
Circadian Misalignment ◽  
Pathological Conditions ◽  
Peripheral Clocks ◽  
Living Organisms ◽  
Almost All

Circadian rhythms are 24-h oscillations driven by a hypothalamic master oscillator that entrains peripheral clocks in almost all cells, tissues and organs. Circadian misalignment, triggered by industrialization and modern lifestyles, has been linked to several pathological conditions, with possible impairment of the quality or even the very existence of life. Living organisms are continuously exposed to air pollutants, and among them, ozone or particulate matters (PMs) are considered to be among the most toxic to human health. In particular, exposure to environmental stressors may result not only in pulmonary and cardiovascular diseases, but, as it has been demonstrated in the last two decades, the skin can also be affected by pollution. In this context, we hypothesize that chronodistruption can exacerbate cell vulnerability to exogenous damaging agents, and we suggest a possible common mechanism of action in deregulation of the homeostasis of the pulmonary, cardiovascular and cutaneous tissues and in its involvement in the development of pathological conditions.

scholarly journals An open‐source sensor‐logger for recording vertical movement in free‐living organisms

2017 ◽  
Vol 9 (3) ◽  
pp. 465-471 ◽  
Author(s):  
J. Ryan Shipley ◽  
Julian Kapoor ◽  
Richard A. Dreelin ◽  
David W. Winkler
Keyword(s):  
Open Source ◽  
Vertical Movement ◽  
Free Living ◽  
Living Organisms
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