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 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 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 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 Comparative Genomics of Trace Element Dependence in Biology

2011 ◽  
Vol 286 (27) ◽  
pp. 23623-23629 ◽  
Author(s):  
Yan Zhang ◽  
Vadim N. Gladyshev
Keyword(s):  
Trace Elements ◽  
Comparative Genomics ◽  
Trace Element ◽  
Evolutionary Dynamics ◽  
Protein Families ◽  
Fundamental Properties ◽  
Recent Advances ◽  
Living Organisms ◽  
Zinc Protein

Biological trace elements are needed in small quantities but are used by all living organisms. A growing list of trace element-dependent proteins and trace element utilization pathways highlights the importance of these elements for life. In this minireview, we focus on recent advances in comparative genomics of trace elements and explore the evolutionary dynamics of the dependence of user proteins on these elements. Many zinc protein families evolved representatives that lack this metal, whereas selenocysteine in proteins is dynamically exchanged with cysteine. Several other elements, such as molybdenum and nickel, have a limited number of user protein families, but they are strictly dependent on these metals. Comparative genomics of trace elements provides a foundation for investigating the fundamental properties, functions, and evolutionary dynamics of trace element dependence in biology.

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

scholarly journals Dynamical analysis of the global elevational diversity gradient in passerine birds reveals a prominent role for highlands as species pumps

2020 ◽  
Author(s):  
Paul van Els ◽  
Leonel Herrera-Alsina ◽  
Alex L. Pigot ◽  
Rampal Etienne
Keyword(s):  
Evolutionary Dynamics ◽  
Strong Support ◽  
High Elevation ◽  
Dynamical Analysis ◽  
Reverse Direction ◽  
Passerine Birds ◽  
Diversification Rates ◽  
Diversity Gradient ◽  
As Species ◽  
Almost All

Abstract Low elevation regions harbor the majority of the world’s species diversity compared to high elevation areas. This global elevational diversity gradient, suggests that lowland species have had more time to diversify, or that net diversification rates have been higher in the lowlands (either due to higher ecological limits or intrinsically higher diversification rates). However, highlands seem to be cradles of diversity as they contain many young endemics, suggesting that their rates of speciation are exceptionally fast. Here, we use a phylogenetic diversification model that accounts for the dispersal of species between different elevations to examine the evolutionary dynamics of the elevational diversity gradient in passerine birds, a group that has radiated globally to occupy almost all elevations and latitudes. We find strong support for a model where passerines diversify at the same rate in the highlands and the lowlands but where the rate of dispersal from high to low elevations is more than twice as fast as in the reverse direction. This suggests that while there is no consistent trend in diversification across elevations, highland regions act as species pumps because the diversity they generate migrates into the lowlands, thus setting up the observed gradient in passerine diversity. This species pump is particularly strong in the tropics, where the inferred rate of speciation is 1.4 times faster than in the temperate zone. We conclude that despite their lower diversity, highland regions are disproportionally important for maintaining diversity in the adjacent lowlands. The extinction of species in the tropical highlands due to rapid climate change this century could thus have major and long-lasting impacts on global passerine diversity.

How to become a parasite without sex chromosomes: a hypothesis for the evolution of Strongyloides spp. and related nematodes

Parasitology ◽  
2014 ◽  
Vol 141 (10) ◽  
pp. 1244-1254 ◽  
Author(s):  
ADRIAN STREIT
Keyword(s):  
Reproductive Strategies ◽  
Life History Traits ◽  
Parasitic Nematode ◽  
Environmental Cues ◽  
Chromatin Diminution ◽  
Free Living ◽  
Parasitic Lifestyle ◽  
Parasitic Worms ◽  
Dauer Larvae ◽  
Parasitic Generation

SUMMARYParasitic lifestyles evolved many times independently. Just within the phylum Nematoda animal parasitism must have arisen at least four times. Switching to a parasitic lifestyle is expected to lead to changes in various life history traits including reproductive strategies. Parasitic nematode worms of the genus Strongyloides represent an interesting example to study these processes because they are still capable of forming facultative free-living generations in between parasitic ones. The parasitic generation consists of females only, which reproduce parthenogenetically. The sex in the progeny of the parasitic worms is determined by environmental cues, which control a, presumably ancestral, XX/XO chromosomal sex determining system. In some species the X chromosome is fused with an autosome and one copy of the X-derived sequences is removed by sex-specific chromatin diminution in males. Here I propose a hypothesis for how today's Strongyloides sp. might have evolved from a sexual free-living ancestor through dauer larvae forming free-living and facultative parasitic intermediate stages.

Environmentally driven escalation of host egg rejection decimates success of an avian brood parasite

2020 ◽  
Vol 31 (6) ◽  
pp. 1316-1325 ◽  
Author(s):  
John M Eadie ◽  
Bruce E Lyon
Keyword(s):  
Large Scale ◽  
Ecological Factors ◽  
Water Levels ◽  
Environmental Drivers ◽  
Egg Rejection ◽  
Vital Rates ◽  
Brood Parasite ◽  
Parasitic Lifestyle ◽  
Almost All ◽  
Rejection Rates

Abstract The black-headed duck (Heteronetta atricapilla) of South America is the only known avian obligate brood parasite with precocial offspring. In Argentina, it relies on two species of coots as primary hosts, which typically reject 35–65% of duck eggs. We show that environmentally driven increases in host egg rejection behavior lead to substantial reductions in the reproductive success of the brood parasite. Episodes of flooding and vegetation loss caused dramatic shifts in host egg-rejection behavior, resulting in rejection (85–95%) of almost all duck eggs. Coots respond to fluctuating water levels by building up their nest, raising their own eggs but leaving duck eggs behind. Coots can apparently recognize parasitic duck eggs, but large-scale rejection is triggered only when hosts must actively make a choice. We use a simple population model to illustrate the unique demographic challenges that black-headed ducks face with their parasitic lifestyle and to explore the potential impact of environmentally induced escalation of egg rejection. Using the best available estimates for key vital rates, we show that obligate parasitism may provide a demographically precarious existence for black-headed ducks, even under benign environmental conditions. Environmentally mediated increases in egg rejection rates by hosts could impact significantly the viability of this enigmatic species of brood parasitic duck. Our results demonstrate that egg rejection rates are not fixed properties of host populations or individuals but are strongly influenced by social and ecological factors. Shifts in these environmental drivers could have important and unforeseen demographic consequences for brood parasites.

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