Illuminating the coevolution of photosynthesis and Bacteria DOI Creative Commons
Arisa Nishihara, Yusuke Tsukatani, Chihiro Azai

et al.

Proceedings of the National Academy of Sciences, Journal Year: 2024, Volume and Issue: 121(25)

Published: June 14, 2024

Life harnessing light energy transformed the relationship between biology and Earth—bringing a massive flux of organic carbon oxidants to Earth’s surface that gave way today’s organotrophy- respiration-dominated biosphere. However, our understanding how life drove this transition has largely relied on geological record; much remains unresolved due complexity paucity genetic record tied photosynthesis. Here, through holistic phylogenetic comparison bacterial domain all photosynthetic machinery (totally spanning >10,000 genomes), we identify evolutionary congruence three independent biological systems—bacteria, (bacterio)chlorophyll-mediated metabolism (chlorophototrophy), fixation—and uncover their intertwined history. Our analyses uniformly mapped progenitors extant light-metabolizing (reaction centers, [bacterio]chlorophyll synthases, magnesium-chelatases) enzymes facilitating Calvin–Benson–Bassham cycle (form I RuBisCO phosphoribulokinase) same ancient Terrabacteria organism near base domain. These phylogenies consistently showed phototrophs ultimately derived from bacterium, last phototroph common ancestor (LPCA). LPCA was non-oxygen-generating (anoxygenic) already possessed fixation two reaction type analogous forms primitive II. Analyses also indicate chlorophototrophy originated before LPCA. We further reconstructed evolution chlorophototrophs/chlorophototrophy post-LPCA, including vertical inheritance in Terrabacteria, rise oxygen-generating one descendant branch Great Oxidation Event, subsequent emergence Cyanobacteria. collectively unveil detailed view coevolution Bacteria having clear with record.

Language: Английский

Divergent evolutionary trajectories of bryophytes and tracheophytes from a complex common ancestor of land plants DOI Creative Commons

Brogan J. Harris,

James Clark, Dominik Schrempf

et al.

Nature Ecology & Evolution, Journal Year: 2022, Volume and Issue: 6(11), P. 1634 - 1643

Published: Sept. 29, 2022

Abstract The origin of plants and their colonization land fundamentally transformed the terrestrial environment. Here we elucidate basis this formative episode in Earth history through patterns lineage, gene genome evolution. We use new fossil calibrations, a relative clade age calibration (informed by horizontal transfer) phylogenomic methods for mapping family origins. Distinct rooting strategies resolve tracheophytes (vascular plants) bryophytes (non-vascular as monophyletic sister groups that diverged during Cambrian, 515–494 million years ago. embryophyte stem is characterized burst innovation, while subsequently experienced an equally dramatic reductive evolution which they lost genes associated with elaboration vasculature stomatal complex. Overall, our analyses reveal extant are both highly derived from more complex ancestral plant. Understanding requires tracing character across diversity modern lineages.

Language: Английский

Citations

107
RNA-targeting CRISPR–Cas systems DOI
Sam P. B. van Beljouw,

Jasper Sanders,

Alicia Rodríguez-Molina

et al.

Nature Reviews Microbiology, Journal Year: 2022, Volume and Issue: 21(1), P. 21 - 34

Published: Sept. 28, 2022

Language: Английский

Citations

70
The nature of the last universal common ancestor and its impact on the early Earth system DOI Creative Commons
Edmund R. R. Moody, Sandra Álvarez-Carretero, Tara Mahendrarajah

et al.

Nature Ecology & Evolution, Journal Year: 2024, Volume and Issue: 8(9), P. 1654 - 1666

Published: July 12, 2024

Abstract The nature of the last universal common ancestor (LUCA), its age and impact on Earth system have been subject vigorous debate across diverse disciplines, often based disparate data methods. Age estimates for LUCA are usually fossil record, varying with every reinterpretation. LUCA’s metabolism has proven equally contentious, some attributing all core metabolisms to LUCA, whereas others reconstruct a simpler life form dependent geochemistry. Here we infer that lived ~4.2 Ga (4.09–4.33 Ga) through divergence time analysis pre-LUCA gene duplicates, calibrated using microbial fossils isotope records under new cross-bracing implementation. Phylogenetic reconciliation suggests had genome at least 2.5 Mb (2.49–2.99 Mb), encoding around 2,600 proteins, comparable modern prokaryotes. Our results suggest was prokaryote-grade anaerobic acetogen possessed an early immune system. Although is sometimes perceived as living in isolation, part established ecological would provided niche other community members hydrogen recycling by atmospheric photochemistry could supported modestly productive ecosystem.

Language: Английский

Citations

54
Genetic manipulation of Patescibacteria provides mechanistic insights into microbial dark matter and the epibiotic lifestyle DOI Creative Commons
Yaxi Wang, Larry A. Gallagher,

Pia A. Andrade

et al.

Cell, Journal Year: 2023, Volume and Issue: 186(22), P. 4803 - 4817.e13

Published: Sept. 7, 2023

Patescibacteria, also known as the candidate phyla radiation (CPR), are a diverse group of bacteria that constitute disproportionately large fraction microbial dark matter. Its few cultivated members, belonging mostly to Saccharibacteria, grow epibionts on host Actinobacteria. Due lack suitable tools, genetic basis this lifestyle and other unique features Patescibacteira remain unexplored. Here, we show Saccharibacteria exhibit natural competence, exploit property for their manipulation. Imaging fluorescent protein-labeled provides high spatiotemporal resolution phenomena accompanying epibiotic growth, transposon-insertion sequencing (Tn-seq) genome-wide screen reveals contribution enigmatic Saccharibacterial genes growth hosts. Finally, leverage metagenomic data provide cutting-edge protein structure-based bioinformatic resources support strain Southlakia epibionticum its corresponding host, Actinomyces israelii, model system unlocking molecular underpinnings lifestyle.

Language: Английский

Citations

47
SingleM and Sandpiper: Robust microbial taxonomic profiles from metagenomic data DOI Creative Commons
Ben J. Woodcroft, Samuel T. N. Aroney, Rossen Zhao

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Jan. 31, 2024

Determining the taxonomy and relative abundance of microorganisms in metagenomic data is a foundational problem microbial ecology. To address limitations existing approaches, we developed ‘SingleM’, which estimates community composition using conserved regions within universal marker genes. SingleM accurately profiles complex communities known species, only tool that detects species without genomic representation, even those representing novel phyla. Given SingleM’s computational efficiency, applied it to 248,559 publicly available metagenomes show vast majority samples from marine, freshwater, sediment soil environments are dominated by lacking representation (median 75.0%). also provides way identify for recovery metagenome-assembled genomes lineages interest, can incorporate user-recovered into its reference database improve profiling resolution. Quantifying full diversity Bacteria Archaea shows genome databases far saturated.

Language: Английский

Citations

40
Insight into the function and evolution of the Wood–Ljungdahl pathway in Actinobacteria DOI Open Access
Jian‐Yu Jiao, Li Fu, Zheng‐Shuang Hua

et al.

The ISME Journal, Journal Year: 2021, Volume and Issue: 15(10), P. 3005 - 3018

Published: May 5, 2021

Language: Английский

Citations

93
Genome-wide analysis of the Firmicutes illuminates the diderm/monoderm transition DOI
Najwa Taïb, Daniela Megrian, Jerzy Witwinowski

et al.

Nature Ecology & Evolution, Journal Year: 2020, Volume and Issue: 4(12), P. 1661 - 1672

Published: Oct. 19, 2020

Language: Английский

Citations

71
Phylogenetic Signal, Congruence, and Uncertainty across Bacteria and Archaea DOI Creative Commons
Carolina A. Martínez-Gutiérrez, Frank O. Aylward

Molecular Biology and Evolution, Journal Year: 2021, Volume and Issue: 38(12), P. 5514 - 5527

Published: Aug. 26, 2021

Abstract Reconstruction of the Tree Life is a central goal in biology. Although numerous novel phyla bacteria and archaea have recently been discovered, inconsistent phylogenetic relationships are routinely reported, many inter-phylum inter-domain evolutionary remain unclear. Here, we benchmark different marker genes often used constructing multidomain trees present set that perform best for constructed from concatenated alignments. We use recently-developed Certainty metrics to assess confidence our results obviate complications traditional bootstrap-based metrics. Given vastly disparate number genomes available archaea, also assessed impact taxon sampling on tree construction. Our demonstrate biases between representation taxonomic groups can dramatically topology resulting trees. Inspection highest-quality supports division most into Terrabacteria Gracilicutes, with Thermatogota Synergistota branching earlier these superphyla. This inclusion Patescibacteria within as sister group Chloroflexota instead basal-branching lineage. For Archaea, three monophyletic lineages (DPANN, Euryarchaeota, TACK/Asgard), although note basal placement DPANN may still represent an artifact caused by biased sequence composition. findings provide robust standardized framework reconstruction be evaluate uncertainty conflicting topologies Life.

Language: Английский

Citations

68
An estimate of the deepest branches of the tree of life from ancient vertically evolving genes DOI Creative Commons
Edmund R. R. Moody, Tara Mahendrarajah, Nina Dombrowski

et al.

eLife, Journal Year: 2022, Volume and Issue: 11

Published: Feb. 22, 2022

Core gene phylogenies provide a window into early evolution, but different sets and analytical methods have yielded substantially views of the tree life. Trees inferred from small set universal core genes typically supported long branch separating archaeal bacterial domains. By contrast, recent analyses broader non-ribosomal suggested that Archaea may be less divergent Bacteria, estimates inter-domain distance are inflated due to accelerated evolution ribosomal proteins along branch. Resolving this debate is key determining diversity domains, shape life, our understanding course cellular evolution. Here, we investigate evolutionary history marker debate. We show reduced Archaea-Bacteria (AB) length result transfers hidden paralogy in expanded set. analysis broad range manually curated datasets an evenly sampled 700 Bacteria reveals current likely underestimate AB substitutional saturation poor model fit; best-performing phylogenetic markers tend support longer lengths; lengths statistically indistinguishable. Furthermore, phylogeny 27 highest-ranked recovers clade DPANN at base places Candidate Phyla Radiation (CPR) within as sister group Chloroflexota.

Language: Английский

Citations

67
Time-resolved comparative molecular evolution of oxygenic photosynthesis DOI Creative Commons
Thomas J. Oliver, Patricia Sánchez‐Baracaldo, Anthony W. D. Larkum

et al.

Biochimica et Biophysica Acta (BBA) - Bioenergetics, Journal Year: 2021, Volume and Issue: 1862(6), P. 148400 - 148400

Published: Feb. 19, 2021

Oxygenic photosynthesis starts with the oxidation of water to O2, a light-driven reaction catalysed by photosystem II. Cyanobacteria are only prokaryotes capable and therefore, it is assumed that origin oxygenic late innovation relative life bioenergetics. However, when exactly originated remains an unanswered question. Here we use phylogenetic analysis study gene duplication event unique II: led evolution core antenna subunits CP43 CP47. We compare changes in rates this those some oldest well-described events history life: namely, leading Alpha Beta catalytic head ATP synthase, divergence archaeal bacterial RNA polymerases ribosomes. also more recent such as Cyanobacteria-specific FtsH metalloprotease radiation Margulisbacteria, Sericytochromatia, Vampirovibrionia, other clades containing anoxygenic phototrophs. demonstrate ancestral II exhibits patterns protein through geological time nearly identical polymerase, or ribosome. Furthermore, sequence reconstruction combination comparative structural biology subunits, provide additional evidence supporting premise had before duplications. Our work suggests photosynthetic closer bioenergetics than can be documented based on phylogenomic species trees alone.

Language: Английский

Citations

65