Two canonically aerobic foraminifera express distinct peroxisomal and mitochondrial metabolisms DOI Creative Commons
Christopher Powers, Fatma Gomaa,

Elizabeth B. Billings

et al.

Frontiers in Marine Science, Journal Year: 2022, Volume and Issue: 9

Published: Dec. 2, 2022

Certain benthic foraminifera thrive in marine sediments with low or undetectable oxygen. Potential survival avenues used by these supposedly aerobic protists include fermentation and anaerobic respiration, although details on their adaptive mechanisms remain elusive. To better understand the metabolic versatility of foraminifera, we studied two species that oxygen-depleted sediments. Here detail, via transcriptomics metatranscriptomics, differential gene expression Nonionella stella Bolivina argentea , collected from Santa Barbara Basin, California, USA, response to varied oxygenation chemical amendments. Organelle-specific reconstructions revealed utilize adaptable mitochondrial peroxisomal metabolism. N. most abundant anoxia characterized lack food vacuoles abundance intracellular lipid droplets, was predicted couple putative beta-oxidation glyoxylate cycle a versatile electron transport system partial TCA cycle. In contrast, B. hypoxia contains vacuoles, gluconeogenesis full but lacks key genes. These adaptations likely confer ecological success while encountering deoxygenation expand our understanding modifications interactions between mitochondria peroxisomes protists.

Language: Английский

Lessons from the deep: mechanisms behind diversification of eukaryotic protein complexes DOI Creative Commons
Galina Prokopchuk, Anzhelika Butenko, Joel B. Dacks

et al.

Biological reviews/Biological reviews of the Cambridge Philosophical Society, Journal Year: 2023, Volume and Issue: 98(6), P. 1910 - 1927

Published: June 19, 2023

Genetic variation is the major mechanism behind adaptation and evolutionary change. As most proteins operate through interactions with other proteins, changes in protein complex composition subunit sequence provide potentially new functions. Comparative genomics can reveal expansions, losses divergence within protein-coding genes, but silico analysis cannot detect substitutions or replacements of entire complexes. Insights into these fundamental processes require broad extensive comparative analyses, from both experimental evidence. Here, we combine data approaches consider gamut possible compositional that arise during evolution, citing examples complete conservation to partial total replacement by functional analogues. We focus part on complexes trypanosomes as they represent one better studied non-animal/non-fungal lineages, extend insights across eukaryotes genomic analysis. argue gene loss plays an important role diversification hence enhancement eukaryotic diversity.

Language: Английский

Citations

12
Anaerobic derivates of mitochondria and peroxisomes in the free-living amoeba Pelomyxa schiedti revealed by single-cell genomics DOI Creative Commons
Kristína Záhonová, Sebastian C. Treitli, Tien Le

et al.

BMC Biology, Journal Year: 2022, Volume and Issue: 20(1)

Published: March 1, 2022

Mitochondria and peroxisomes are the two organelles that most affected during adaptation to microoxic or anoxic environments. known transform into anaerobic mitochondria, hydrogenosomes, mitosomes, various transition stages in between, collectively called mitochondrion-related (MROs), which vary enzymatic capacity. Anaerobic were identified only recently, their putatively conserved function seems be metabolism of inositol. The group Archamoebae includes anaerobes bearing both MROs, specifically hydrogenosomes free-living Mastigamoeba balamuthi mitosomes human pathogen Entamoeba histolytica, while within third lineage represented by Pelomyxa remain uncharacterized.

Language: Английский

Citations

19
Group-specific functional patterns of mitochondrion-related organelles shed light on their multiple transitions from mitochondria in ciliated protists DOI
Zhicheng Chen, Jia Li, Dayana E. Salas‐Leiva

et al.

Marine Life Science & Technology, Journal Year: 2022, Volume and Issue: 4(4), P. 609 - 623

Published: Nov. 21, 2022

Language: Английский

Citations

17
A Mitosome With Distinct Metabolism in the Uncultured Protist ParasiteParamikrocytos canceri(Rhizaria, Ascetosporea) DOI Creative Commons
Ioana Onut Brännström, Courtney W. Stairs, Karla Iveth Aguilera Campos

et al.

Genome Biology and Evolution, Journal Year: 2023, Volume and Issue: 15(3)

Published: Feb. 11, 2023

Abstract Ascetosporea are endoparasites of marine invertebrates that include economically important pathogens aquaculture species. Owing to their often-minuscule cell sizes, strict intracellular lifestyle, lack cultured representatives and minimal availability molecular data, these unicellular parasites remain poorly studied. Here, we sequenced assembled the genome transcriptome Paramikrocytos canceri, an endoparasite isolated from European edible crab Cancer pagurus. Using bioinformatic predictions, show P. canceri likely possesses a mitochondrion-related organelle (MRO) with highly reduced metabolism, resembling mitosomes other but key differences. Like mitosomes, this MRO is predicted have metabolic capacity organellar function in iron–sulfur cluster (ISC) pathway-mediated Fe–S biosynthesis. However, uniquely produce ATP via partial glycolytic pathway synthesize phospholipids de novo through CDP-DAG pathway. Heterologous gene expression confirmed proteins ISC pathways retain mitochondrial targeting sequences recognized by yeast mitochondria. This represents unique combination MRO, including first reported case mitosome-like able novo. Some phospholipids, such as phosphatidylserine, vital protist invade host apoptotic mimicry.

Language: Английский

Citations

11
An argument for using anaerobes as microbial cell factories to advance synthetic biology and biomanufacturing DOI Creative Commons
Thomas S. Lankiewicz, Nathalie H. Elisabeth, David L. Valentine

et al.

AIChE Journal, Journal Year: 2025, Volume and Issue: 71(6)

Published: Feb. 25, 2025

Abstract Anaerobes thrive in the absence of oxygen and are an untapped reservoir biotechnological potential. Therefore, bioprospecting efforts focused on anaerobic microbial diversity could rapidly uncover new enzymes, pathways, chassis organisms to drive biotechnology innovation. Despite their potential utility, fermenters viewed as inefficient from a biochemical perspective because metabolisms produce fewer ATP (~2) per molecule glucose processed than heterotrophic respirers (~32–38 ATP). While aerobes excel at generation, they often less efficient anaerobes processes that compete with generation for cellular resources. This highlights how adaptations advantageous synthetic biology biomanufacturing applications through engineering cell factories. We further highlight emerging bioprocessing, including use lignocellulosic human environmental health, value‐added bioproduction.

Language: Английский

Citations

0
Convergent pathways of reductive mitochondrial evolution characterised with hypercubic inference DOI Creative Commons
Robert C. Glastad, Iain G. Johnston

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: May 4, 2025

Abstract For a striking example of mitochondrial behaviour beyond ATP generation, consider mitochondrion-related organelles (MROs). Hydrogenosomes, mitosomes, and other reduced forms have evolved through the loss physical functional features, from individual ETC complexes to oxidative phosphorylaytion very ability produce (and further). Reduction mitochondria is dramatic convergent evolution, occuring in every eukaryotic kingdom many parallel times. Here, we use hypercubic inference, class methods evolutionary accumulation modelling (EvAM), explore pathways reduction across eukaryotes. We find that most MRO diversity can be explained by small variations on two distinct pathways, starting with either Complex I or Complexes III/IV, which tend proceed over different characteristic timescales. show clades, including ciliates apicomplexans, reflect particular instances these pathways. Using metabolic modelling, connect structure impact changes involved, suggesting plausible explanation for dramatically nature reductive evolution. discuss this approach connection related theory genetic organisms.

Language: Английский

Citations

0
Evolving Perspective on the Origin and Diversification of Cellular Life and the Virosphere DOI Creative Commons
Anja Spang, Tara Mahendrarajah, Pierre Offre

et al.

Genome Biology and Evolution, Journal Year: 2022, Volume and Issue: 14(6)

Published: Feb. 25, 2022

Abstract The tree of life (TOL) is a powerful framework to depict the evolutionary history cellular organisms through time, from our microbial origins diversification multicellular eukaryotes that shape visible biosphere today. During past decades, perception TOL has fundamentally changed, in part, due profound methodological advances, which allowed more objective approach studying organismal and viral diversity led discovery major new branches as well lineages. Phylogenetic comparative genomics analyses these data have, among others, revolutionized understanding deep roots life, origin eukaryotic cell, diversity, origin, viruses. In this review, we provide an overview some recent discoveries on their viruses discuss variety complementary techniques consider crucial for making further progress its interconnection with virosphere.

Language: Английский

Citations

15
Extreme mitochondrial reduction in a novel group of free-living metamonads DOI Creative Commons
Shelby K. Williams, Jon Jerlström-Hultqvist, Yana Eglit

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: May 4, 2023

Summary Metamonads are a diverse group of heterotrophic microbial eukaryotes adapted to living in hypoxic environments. All metamonads but one harbour metabolically altered ‘mitochondrion-related organelles’ (MROs) with reduced functions relative aerobic mitochondria, however the degree reduction varies markedly over metamonad tree. To further investigate MRO diversity, we generated high quality draft genomes, transcriptomes, and predicted proteomes for five recently discovered free-living metamonads. Phylogenomic analyses placed these organisms informally named ‘BaSk’ (Barthelonids+Skoliomonads) clade, which emerges as deeply branching sister Fornicata, phylum that includes parasitic flagellates. Extensive bioinformatic manually curated gene models showed have extremely comparison other Loss mitochondrial iron-sulfur cluster (ISC) assembly system some this appears be linked acquisition their common ancestral lineage SUF-like minimal (SMS) Fe/S pathway through lateral transfer (LGT). One isolates, Skoliomonas litria , undergone having lost all known pathways. No proteins were confidently assigned proteome organism suggesting organelle has been lost. The extreme observed within anaerobic protistan clade is unprecedented demonstrates functions, under conditions, may completely even organisms.

Language: Английский

Citations

7
Characterization of Skoliomonas gen. nov., a haloalkaliphilic anaerobe related to barthelonids (Metamonada) DOI Creative Commons
Yana Eglit, Shelby K. Williams, Andrew J. Roger

et al.

Journal of Eukaryotic Microbiology, Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 3, 2024

Abstract Metamonads are a large and exclusively anaerobic group of protists. Additionally, they one the three clades proposed to ancestrally possess an “excavate” cell morphology, with conspicuous ventral groove accompanied by posterior flagellum vane. Here, we cultivate characterize four bacterivorous flagellates from hypersaline alkaline soda lake environments, which represent novel clade. Small subunit ribosomal RNA (SSU rRNA) gene phylogenies support recent phylogenomic analyses in placing them as sister barthelonids, that is itself or deeply branching within Fornicata (Metamonada). The new isolates have distinctive morphology: hunchbacked body traversed narrow ending opening recurrent cytopharynx. right margin defined thin “lip.” bears wide ventral‐facing elongate cytopharynx shared barthelonids. We describe isolate Skoliomonas litria , gen. et sp. nov. Further investigation their mitochondrial‐related organelles (MROs) detailed ultrastructural studies would be important understanding adaptation conditions Metamonads—especially fornicates—as well evolution architecture.

Language: Английский

Citations

2
Novel Mode Engineering for β-Alanine Production in Escherichia coli with the Guide of Adaptive Laboratory Evolution DOI Creative Commons

Jian Xu,

Li Zhou, Meng Yin

et al.

Microorganisms, Journal Year: 2021, Volume and Issue: 9(3), P. 600 - 600

Published: March 15, 2021

The strategy of anaerobic biosynthesis β-alanine by Escherichia coli (E. coli) has been reported. However, the low energy production under condition limited cell growth and then affected efficiency β-alanine. Here, adaptive laboratory evolution was carried out to improve E. lacking phosphoenolpyruvate carboxylase condition. Five mutants were isolated analyzed. Sequence analysis showed that most consistent genetic mutations among related with pyruvate accumulation, indicating accumulation enabled lethal parent. It is possible accumulated provides sufficient precursors for generation CO2 fixing reaction catalyzed carboxykinase. B0016-100BB (B0016-090BB, recE::FRT, mhpF::FRT, ykgF::FRT, mhpB:: mhpB *, mhpD:: mhpD rcsA:: rcsA *) engineered based on Along recruitment glycerol as sole carbon source, 1.07 g/L generated B0016-200BB (B0016-100BB, aspA::FRT) harboring pET24a-panD-AspDH, which used overexpression two key enzymes in fermentation process. Compared starting strain, can hardly generate condition, factory significantly improved.

Language: Английский

Citations

12