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

ATP synthase evolution on a cross-braced dated tree of life DOI Creative Commons
Tara Mahendrarajah, Edmund R. R. Moody, Dominik Schrempf

et al.

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: Nov. 17, 2023

Abstract The timing of early cellular evolution, from the divergence Archaea and Bacteria to origin eukaryotes, is poorly constrained. ATP synthase complex thought have originated prior Last Universal Common Ancestor (LUCA) analyses genes, together with ribosomes, played a key role in inferring rooting tree life. We reconstruct evolutionary history synthases using an expanded taxon sampling set develop phylogenetic cross-bracing approach, constraining equivalent speciation nodes be contemporaneous, based on imprint endosymbioses ancient gene duplications. This approach results highly resolved, dated species establishes absolute timeline for evolution. Our show that into F- A/V-type lineages was very event evolution dating back more than 4 Ga, potentially predating diversification Bacteria. cross-braced, life also provides insight recent transitions including eukaryogenesis, showing eukaryotic nuclear mitochondrial diverged their closest archaeal (2.67-2.19 Ga) bacterial (2.58-2.12 relatives at approximately same time, slightly longer stem-lineage.

Language: Английский

Citations

42
Extreme environments offer an unprecedented opportunity to understand microbial eukaryotic ecology, evolution, and genome biology DOI Creative Commons
Hannah Rappaport, Angela Oliverio

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: Aug. 16, 2023

Abstract Research in extreme environments has substantially expanded our understanding of the ecology and evolution life on Earth, but a major group organisms been largely overlooked: microbial eukaryotes (i.e., protists). In this Perspective, we summarize data from over 80 studies protists identify focal lineages that are significant interest for further study, including clades within Echinamoebida, Heterolobosea, Radiolaria, Haptophyta, Oomycota, Cryptophyta. We argue prime sampling targets to fill gaps eukaryotic tree increase ecology, metabolism, genome architecture, life.

Language: Английский

Citations

28
Parallel functional reduction in the mitochondria of apicomplexan parasites DOI Creative Commons
Varsha Mathur, Kevin C. Wakeman, Patrick J. Keeling

et al.

Current Biology, Journal Year: 2021, Volume and Issue: 31(13), P. 2920 - 2928.e4

Published: May 10, 2021

Language: Английский

Citations

46
Gregarine single-cell transcriptomics reveals differential mitochondrial remodeling and adaptation in apicomplexans DOI Creative Commons
Eric D. Salomaki, Kristina X. Terpis, Sonja Rueckert

et al.

BMC Biology, Journal Year: 2021, Volume and Issue: 19(1)

Published: April 16, 2021

Apicomplexa is a diverse phylum comprising unicellular endobiotic animal parasites and contains some of the most well-studied microbial eukaryotes including devastating human pathogens Plasmodium falciparum Cryptosporidium hominis. In contrast, data on invertebrate-infecting gregarines remains sparse their evolutionary relationship to other apicomplexans obscure. Most retain highly modified plastid, while mitochondria remain metabolically conserved. spp. inhabit an anaerobic host-gut environment represent known exception, having completely lost plastid retaining extremely reduced mitochondrion that has its genome. Recent advances in single-cell sequencing have enabled first broad genome-scale explorations gregarines, providing evidence differential retention throughout group. However, little about metabolic capacity gregarine mitochondria.

Language: Английский

Citations

42
Anaerobic ciliates as a model group for studying symbioses in oxygen‐depleted environments DOI
Johana Rotterová, Virginia P. Edgcomb, Ivan Čepička

et al.

Journal of Eukaryotic Microbiology, Journal Year: 2022, Volume and Issue: 69(5)

Published: March 24, 2022

Abstract Anaerobiosis has independently evolved in multiple lineages of ciliates, allowing them to colonize a variety anoxic and oxygen‐depleted habitats. Anaerobic ciliates commonly form symbiotic relationships with various prokaryotes, including methanogenic archaea members several bacterial groups. The hypothesized functions these ecto‐ endosymbionts include the symbiont utilizing ciliate's fermentative end products increase host's anaerobic metabolic efficiency, or directly providing host energy by denitrification photosynthesis. host, turn, may protect from competition, environment, predation. Despite rapid advances sampling, molecular, microscopy methods, as well associated broadening known diversity many aspects ciliate symbioses, specificity coevolution, remain largely unexplored. Nevertheless, number comparative genomic transcriptomic analyses targeting their symbionts on rise, insights into nature symbioses evolution transition obligate anaerobiosis continue deepen. This review summarizes current body knowledge regarding complex symbionts, role significance ecosystem‐level processes.

Language: Английский

Citations

34
Protists: the hidden ecosystem players in a wetland rice field soil DOI

Jun Murase,

Rasit Asiloglu

Biology and Fertility of Soils, Journal Year: 2023, Volume and Issue: 60(6), P. 773 - 787

Published: Feb. 14, 2023

Language: Английский

Citations

21
Predicting microbe organisms using data of living micro forms of life and hybrid microbes classifier DOI Creative Commons
Ali Raza, Furqan Rustam, Hafeez Ur Rehman Siddiqui

et al.

PLoS ONE, Journal Year: 2023, Volume and Issue: 18(4), P. e0284522 - e0284522

Published: April 20, 2023

Microbe organisms make up approximately 60% of the earth's living matter and human body is home to millions microbe organisms. Microbes are microbial threats health may lead several diseases in humans like toxoplasmosis malaria. The microbiological disease widespread, with a seroprevalence 3.6-84% sub-Saharan Africa. This necessitates an automated approach for detection. primary objective this study predict body. A novel hybrid microbes classifier (HMC) proposed which based on decision tree extra using voting criteria. Experiments involve different machine learning deep models detecting ten microforms life. Results suggest that HMC achieves 98% accuracy score, geometric mean 97% precision Cohen Kappa score. model outperforms employed models, as well as, existing state-of-the-art models. Moreover, k-fold cross-validation corroborates results well. research helps microbiologists identify type high prevents many through early

Language: Английский

Citations

18
Extreme mitochondrial reduction in a novel group of free-living metamonads DOI Creative Commons
Shelby K. Williams, Jon Jerlström-Hultqvist, Yana Eglit

et al.

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: Aug. 9, 2024

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, however the degree reduction varies. Here, we generate high-quality draft genomes, transcriptomes, and predicted proteomes for five recently discovered free-living metamonads. Phylogenomic analyses placed these organisms name 'BaSk' (Barthelonids+Skoliomonads) clade, deeply branching sister Fornicata, phylum that includes parasitic flagellates. Bioinformatic gene models shows have extremely MRO comparison other Loss mitochondrial iron-sulfur cluster assembly system some this appears be linked acquisition their common ancestral lineage SUF-like minimal Fe/S pathway by lateral transfer. One isolates, Skoliomonas litria, lost all known pathways. No proteins were confidently assigned proteome organism suggesting organelle has been lost. The extreme observed within anaerobic protistan clade demonstrates functions may completely even organisms. Mitochondria essential cellular components found animals, plants, fungi, protists. This study reports what is believed first example complete loss organism, providing insights into evolutionary plasticity eukaryotic cells.

Language: Английский

Citations

6
Highly flexible metabolism of the marine euglenozoan protist Diplonema papillatum DOI Creative Commons
Ingrid Škodová‐Sveráková, Kristína Záhonová, Valéria Juricová

et al.

BMC Biology, Journal Year: 2021, Volume and Issue: 19(1)

Published: Nov. 24, 2021

The phylum Euglenozoa is a group of flagellated protists comprising the diplonemids, euglenids, symbiontids, and kinetoplastids. diplonemids are highly abundant speciose, recent tools have rendered best studied representative, Diplonema papillatum, genetically tractable. However, despite high diversity their lifestyles, ecological functions, even primary energy source mostly unknown.

Language: Английский

Citations

28
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