scholarly journals Diversity and origins of anaerobic metabolism in mitochondria and related organelles

2015 ◽  
Vol 370 (1678) ◽  
pp. 20140326 ◽  
Author(s):  
Courtney W. Stairs ◽  
Michelle M. Leger ◽  
Andrew J. Roger
Keyword(s):  
Metabolic Pathways ◽  
Anaerobic Metabolism ◽  
Low Oxygen ◽  
Metabolic Potential ◽  
Free Living ◽  
Eukaryotic Diversity ◽  
The Past ◽  
Microbial Eukaryotes ◽  
Sequencing Studies ◽  
Diversity Of Life

Across the diversity of life, organisms have evolved different strategies to thrive in hypoxic environments, and microbial eukaryotes (protists) are no exception. Protists that experience hypoxia often possess metabolically distinct mitochondria called mitochondrion-related organelles (MROs). While there are some common metabolic features shared between the MROs of distantly related protists, these organelles have evolved independently multiple times across the breadth of eukaryotic diversity. Until recently, much of our knowledge regarding the metabolic potential of different MROs was limited to studies in parasitic lineages. Over the past decade, deep-sequencing studies of free-living anaerobic protists have revealed novel configurations of metabolic pathways that have been co-opted for life in low oxygen environments. Here, we provide recent examples of anaerobic metabolism in the MROs of free-living protists and their parasitic relatives. Additionally, we outline evolutionary scenarios to explain the origins of these anaerobic pathways in eukaryotes.

scholarly journals Metabolic Diversity and Evolutionary History of the Archaeal Phylum “Candidatus Micrarchaeota” Uncovered from a Freshwater Lake Metagenome

2020 ◽  
Vol 86 (23) ◽  
Author(s):  
Vitaly V. Kadnikov ◽  
Alexander S. Savvichev ◽  
Andrey V. Mardanov ◽  
Alexey V. Beletsky ◽  
Artem V. Chupakov ◽  
...  
Keyword(s):  
Metabolic Pathways ◽  
Mine Drainage ◽  
De Novo ◽  
Group Analysis ◽  
Freshwater Lake ◽  
Ancestral State ◽  
Metabolic Potential ◽  
Free Living ◽  
Nucleotide Biosynthesis ◽  
Generation Mechanisms

ABSTRACT Acidophilic archaea of the archaeal Richmond Mine acidophilic nanoorganisms (ARMAN) group from the uncultured candidate phylum “Candidatus Micrarchaeota” have small genomes and cell sizes and are known to be metabolically dependent and physically associated with their Thermoplasmatales hosts. However, phylogenetically diverse “Ca. Micrarchaeota” are widely distributed in various nonacidic environments, and it remains uncertain because of the lack of complete genomes whether they are also devoted to a partner-dependent lifestyle. Here, we obtained nine metagenome-assembled genomes of “Ca. Micrarchaeota” from the sediments of a meromictic freshwater lake, including a complete, closed 1.2 Mbp genome of “Ca. Micrarchaeota” Sv326, an archaeon phylogenetically distant from the ARMAN lineage. Genome analysis revealed that, contrary to ARMAN “Ca. Micrarchaeota,” the Sv326 archaeon has complete glycolytic pathways and ATP generation mechanisms in substrate phosphorylation reactions, the capacities to utilize some sugars and amino acids as substrates, and pathways for de novo nucleotide biosynthesis but lacked an aerobic respiratory chain. We suppose that Sv326 is a free-living scavenger rather than an obligate parasite/symbiont. Comparative analysis of “Ca. Micrarchaeota” genomes representing different order-level divisions indicated that evolution of the “Ca. Micrarchaeota” from a free-living “Candidatus Diapherotrites”-like ancestor involved losses of important metabolic pathways in different lineages and gains of specific functions in the course of adaptation to a partner-dependent lifestyle and specific environmental conditions. The ARMAN group represents the most pronounced case of genome reduction and gene loss, while the Sv326 lineage appeared to be rather close to the ancestral state of the “Ca. Micrarchaeota” in terms of metabolic potential. IMPORTANCE The recently described superphylum DPANN includes several phyla of uncultivated archaea with small cell sizes, reduced genomes, and limited metabolic capabilities. One of these phyla, “Ca. Micrarchaeota,” comprises an enigmatic group of archaea found in acid mine drainage environments, the archaeal Richmond Mine acidophilic nanoorganisms (ARMAN) group. Analysis of their reduced genomes revealed the absence of key metabolic pathways consistent with their partner-associated lifestyle, and physical associations of ARMAN cells with their hosts were documented. However, “Ca. Micrarchaeota” include several lineages besides the ARMAN group found in nonacidic environments, and none of them have been characterized. Here, we report a complete genome of “Ca. Micrarchaeota” from a non-ARMAN lineage. Analysis of this genome revealed the presence of metabolic capacities lost in ARMAN genomes that could enable a free-living lifestyle. These results expand our understanding of genetic diversity, lifestyle, and evolution of “Ca. Micrarchaeota.”

scholarly journals Identification of the pathway of Rhodoquinone biosynthesis in C.elegans

2019 ◽  
Author(s):  
Samantha Del Borrello ◽  
Margot Lautens ◽  
Kathleen Dolan ◽  
June H. Tan ◽  
Mark A. Spensley ◽  
...  
Keyword(s):  
Metabolic Pathways ◽  
Animal Species ◽  
Anaerobic Metabolism ◽  
Low Oxygen ◽  
Electron Carrier ◽  
Parasitic Helminths ◽  
New Class ◽  
Hypoxic Conditions ◽  
First Time ◽  
Made In

AbstractParasitic helminths infect over a billion humans. To survive in the low oxygen environment of their hosts, these parasites use unusual anaerobic metabolism. This requires Rhodoquinone (RQ), an electron carrier that is made by very few animal species — crucially it is not present in any parasitic hosts. RQ synthesis is thus an ideal target for anthelmintics but little is known about how RQ is made and no drugs are known to block RQ synthesis. C.elegans makes RQ and can use RQ-dependent metabolic pathways — here, we use C.elegans genetics to identify the pathway for RQ synthesis and show that C.elegans requires RQ for survival in hypoxic conditions. Finally, we establish a robust assay for drugs that block RQ-dependent metabolism. This study identifies for the first time how RQ is made in any animal and establishes a novel assay that can drive the development of a new class of anthelmintic drugs.

Brain-eating Amoebae Infection: Challenges and Opportunities in Chemotherapy

2019 ◽  
Vol 19 (12) ◽  
pp. 980-987 ◽  
Author(s):  
Mohammad Ridwane Mungroo ◽  
Ayaz Anwar ◽  
Naveed Ahmed Khan ◽  
Ruqaiyyah Siddiqui
Keyword(s):  
Mortality Rate ◽  
Free Living ◽  
Outdoor Activities ◽  
The Past ◽  
Free Living Amoeba ◽  
Challenges And Opportunities ◽  
Life Threatening ◽  
The Central Nervous System ◽  
Living Nature ◽  
Treatment And Diagnosis

Pathogenic free-living amoeba are known to cause a devastating infection of the central nervous system and are often referred to as “brain-eating amoebae”. The mortality rate of more than 90% and free-living nature of these amoebae is a cause for concern. It is distressing that the mortality rate has remained the same over the past few decades, highlighting the lack of interest by the pharmaceutical industry. With the threat of global warming and increased outdoor activities of public, there is a need for renewed interest in identifying potential anti-amoebic compounds for successful prognosis. Here, we discuss the available chemotherapeutic options and opportunities for potential strategies in the treatment and diagnosis of these life-threatening infections.

scholarly journals Cytokinin N-glucosides: Occurrence, Metabolism and Biological Activities in Plants

Biomolecules ◽  
2020 ◽  
Vol 11 (1) ◽  
pp. 24
Author(s):  
Eva Pokorná ◽  
Tomáš Hluska ◽  
Petr Galuszka ◽  
H. Tucker Hallmark ◽  
Petre I. Dobrev ◽  
...  
Keyword(s):  
Metabolic Pathways ◽  
Growth And Development ◽  
Biological Activities ◽  
Physiological Effects ◽  
Inhibitory Effects ◽  
Plant Growth And Development ◽  
The Past ◽  
Complex Process ◽  
Considerable Impact ◽  
Physiological Impact

Cytokinins (CKs) are a class of phytohormones affecting many aspects of plant growth and development. In the complex process of CK homeostasis in plants, N-glucosylation represents one of the essential metabolic pathways. Its products, CK N7- and N9-glucosides, have been largely overlooked in the past as irreversible and inactive CK products lacking any relevant physiological impact. In this work, we report a widespread distribution of CK N-glucosides across the plant kingdom proceeding from evolutionary older to younger plants with different proportions between N7- and N9-glucosides in the total CK pool. We show dramatic changes in their profiles as well as in expression levels of the UGT76C1 and UGT76C2 genes during Arabidopsis ontogenesis. We also demonstrate specific physiological effects of CK N-glucosides in CK bioassays including their antisenescent activities, inhibitory effects on root development, and activation of the CK signaling pathway visualized by the CK-responsive YFP reporter line, TCSv2::3XVENUS. Last but not least, we present the considerable impact of CK N7- and N9-glucosides on the expression of CK-related genes in maize and their stimulatory effects on CK oxidase/dehydrogenase activity in oats. Our findings revise the apparent irreversibility and inactivity of CK N7- and N9-glucosides and indicate their involvement in CK evolution while suggesting their unique function(s) in plants.

scholarly journals Unraveling the Metabolic Potential of Asgardarchaeota in a Sediment from the Mediterranean Hydrocarbon-Contaminated Water Basin Mar Piccolo (Taranto, Italy)

2021 ◽  
Vol 9 (4) ◽  
pp. 859
Author(s):  
Andrea Firrincieli ◽  
Andrea Negroni ◽  
Giulio Zanaroli ◽  
Martina Cappelletti
Keyword(s):  
Archaeal Community ◽  
Hydrocarbon Biodegradation ◽  
Natural Ecosystems ◽  
Central Mediterranean ◽  
Metabolic Potential ◽  
Metabolic Role ◽  
Sequencing Studies ◽  
Terrestrial Environments ◽  
Metagenome Sequencing ◽  
Aliphatic And Aromatic Hydrocarbons

Increasing number of metagenome sequencing studies have proposed a central metabolic role of still understudied Archaeal members in natural and artificial ecosystems. However, their role in hydrocarbon cycling, particularly in the anaerobic biodegradation of aliphatic and aromatic hydrocarbons, is still mostly unknown in both marine and terrestrial environments. In this work, we focused our study on the metagenomic characterization of the archaeal community inhabiting the Mar Piccolo (Taranto, Italy, central Mediterranean) sediments heavily contaminated by petroleum hydrocarbons and polychlorinated biphenyls (PCB). Among metagenomic bins reconstructed from Mar Piccolo microbial community, we have identified members of the Asgardarchaeota superphylum that has been recently proposed to play a central role in hydrocarbon cycling in natural ecosystems under anoxic conditions. In particular, we found members affiliated with Thorarchaeota, Heimdallarchaeota, and Lokiarchaeota phyla and analyzed their genomic potential involved in central metabolism and hydrocarbon biodegradation. Metabolic prediction based on metagenomic analysis identified the malonyl-CoA and benzoyl-CoA routes as the pathways involved in aliphatic and aromatic biodegradation in these Asgardarchaeota members. This is the first study to give insight into the archaeal community functionality and connection to hydrocarbon degradation in marine sediment historically contaminated by hydrocarbons.

scholarly journals A Transcriptomic Approach to the Metabolism of Tetrapyrrolic Photosensitizers in a Marine Annelid

Molecules ◽  
2021 ◽  
Vol 26 (13) ◽  
pp. 3924
Author(s):  
Maria Leonor Santos ◽  
Mariaelena D’Ambrosio ◽  
Ana P. Rodrigo ◽  
A. Jorge Parola ◽  
Pedro M. Costa
Keyword(s):  
Metabolic Pathways ◽  
Molecular Networks ◽  
Bile Pigments ◽  
Rna Seq ◽  
The Past ◽  
Wide Range ◽  
Genes Encoding ◽  
Organ Specific ◽  
Bright Green ◽  
Green Coloration

The past decade has seen growing interest in marine natural pigments for biotechnological applications. One of the most abundant classes of biological pigments is the tetrapyrroles, which are prized targets due their photodynamic properties; porphyrins are the best known examples of this group. Many animal porphyrinoids and other tetrapyrroles are produced through heme metabolic pathways, the best known of which are the bile pigments biliverdin and bilirubin. Eulalia is a marine Polychaeta characterized by its bright green coloration resulting from a remarkably wide range of greenish and yellowish tetrapyrroles, some of which have promising photodynamic properties. The present study combined metabolomics based on HPLC-DAD with RNA-seq transcriptomics to investigate the molecular pathways of porphyrinoid metabolism by comparing the worm’s proboscis and epidermis, which display distinct pigmentation patterns. The results showed that pigments are endogenous and seemingly heme-derived. The worm possesses homologs in both organs for genes encoding enzymes involved in heme metabolism such as ALAD, FECH, UROS, and PPOX. However, the findings also indicate that variants of the canonical enzymes of the heme biosynthesis pathway can be species- and organ-specific. These differences between molecular networks contribute to explain not only the differential pigmentation patterns between organs, but also the worm’s variety of novel endogenous tetrapyrrolic compounds.

scholarly journals Free-Living User Perspectives on Musculoskeletal Pain and Patient-Reported Mobility With Passive and Powered Prosthetic Ankle-Foot Components: A Pragmatic, Exploratory Cross-Sectional Study

2022 ◽  
Vol 2 ◽  
Author(s):  
Andreas Kannenberg ◽  
Arri R. Morris ◽  
Karl D. Hibler
Keyword(s):  
Musculoskeletal Pain ◽  
Knee Pain ◽  
Online Survey ◽  
Rating Scales ◽  
Living Environment ◽  
Rank Test ◽  
Recall Bias ◽  
Free Living ◽  
The Past ◽  
Patient Reported

IntroductionStudies with a powered prosthetic ankle-foot (PwrAF) found a reduction in sound knee loading compared to passive feet. Therefore, the aim of the present study was to determine whether anecdotal reports on reduced musculoskeletal pain and improved patient-reported mobility were isolated occurrences or reflect a common experience in PwrAF users.MethodsTwo hundred and fifty individuals with transtibial amputation (TTA) who had been fitted a PwrAF in the past were invited to an online survey on average sound knee, amputated side knee, and low-back pain assessed with numerical pain rating scales (NPRS), the PROMIS Pain Interference scale, and the PLUS-M for patient-reported mobility in the free-living environment. Subjects rated their current foot and recalled the ratings for their previous foot. Recalled scores were adjusted for recall bias by clinically meaningful amounts following published recommendations. Statistical comparisons were performed using Wilcoxon's signed rank test.ResultsForty-six subjects, all male, with unilateral TTA provided data suitable for analysis. Eighteen individuals (39%) were current PwrAF users, whereas 28 subjects (61%) had reverted to a passive foot. After adjustment for recall bias, current PwrAF users reported significantly less sound knee pain than they recalled for use of a passive foot (−0.5 NPRS, p = 0.036). Current PwrAF users who recalled sound knee pain ≥4 NPRS with a passive foot reported significant and clinically meaningful improvements in sound knee pain (−2.5 NPRS, p = 0.038) and amputated side knee pain (−3 NPRS, p = 0.042). Current PwrAF users also reported significant and clinically meaningful improvements in patient-reported mobility (+4.6 points PLUS-M, p = 0.016). Individuals who had abandoned the PwrAF did not recall any differences between the feet.DiscussionCurrent PwrAF users reported significant and clinically meaningful improvements in patient-reported prosthetic mobility as well as sound knee and amputated side knee pain compared to recalled mobility and pain with passive feet used previously. However, a substantial proportion of individuals who had been fitted such a foot in the past did not recall improvements and had reverted to passive feet. The identification of individuals with unilateral TTA who are likely to benefit from a PwrAF remains a clinical challenge and requires further research.

scholarly journals Chronic Myelomonocytic Leukemia—Hematopathology Perspective

2021 ◽  
Author(s):  
Siba El Hussein ◽  
Sa A. Wang ◽  
Naveen Pemmaraju ◽  
Joseph D. Khoury ◽  
Sanam Loghavi
Keyword(s):  
Risk Stratification ◽  
Large Scale ◽  
Chronic Myelomonocytic Leukemia ◽  
Clinical Implications ◽  
The Past ◽  
Genomic Landscape ◽  
Sequencing Studies ◽  
Myelomonocytic Leukemia ◽  
Insight Into

ABSTRACT Our understanding of chronic myelomonocytic leukemia (CMML) has evolved tremendously over the past decade. Large-scale sequencing studies have led to increased insight into the genomic landscape of CMML and clinical implications of these changes. This in turn has resulted in refined and improved risk stratification models, which to date remain versatile and subject to remodeling, as new and evolving studies continue to refine our understanding of this disease. In this article, we present an up-to-date review of CMML from a hematopathology perspective, while providing a clinically practical summary that sheds light on the constant evolution of our understanding of this disease.

Pyrophosphate as an alternative energy currency in plants

2021 ◽  
Vol 478 (8) ◽  
pp. 1515-1524
Author(s):  
Abir U. Igamberdiev ◽  
Leszek A. Kleczkowski
Keyword(s):  
Metabolic Pathways ◽  
Energy Efficient ◽  
Alternative Energy ◽  
Plant Cells ◽  
Atp Synthesis ◽  
Continuous Operation ◽  
Low Oxygen ◽  
Pyruvate Phosphate Dikinase ◽  
Oxygen Stress ◽  
Membrane Bound

In the conditions of [Mg2+] elevation that occur, in particular, under low oxygen stress and are the consequence of the decrease in [ATP] and increase in [ADP] and [AMP], pyrophosphate (PPi) can function as an alternative energy currency in plant cells. In addition to its production by various metabolic pathways, PPi can be synthesized in the combined reactions of pyruvate, phosphate dikinase (PPDK) and pyruvate kinase (PK) by so-called PK/PPDK substrate cycle, and in the reverse reaction of membrane-bound H+-pyrophosphatase, which uses the energy of electrochemical gradients generated on tonoplast and plasma membrane. The PPi can then be consumed in its active forms of MgPPi and Mg2PPi by PPi-utilizing enzymes, which require an elevated [Mg2+]. This ensures a continuous operation of glycolysis in the conditions of suppressed ATP synthesis, keeping metabolism energy efficient and less dependent on ATP.

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