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

CPR bacteria and DPANN archaea play pivotal roles in response of microbial community to antibiotic stress in groundwater DOI

Moran Tang,

Qian Chen, Haohui Zhong

et al.

Water Research, Journal Year: 2024, Volume and Issue: 251, P. 121137 - 121137

Published: Jan. 21, 2024

Language: Английский

Citations

14
Valid publication of names of two domains and seven kingdoms of prokaryotes DOI
Markus Göker, Aharon Oren

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Journal Year: 2024, Volume and Issue: 74(1)

Published: Jan. 22, 2024

The International Code of Nomenclature Prokaryotes (ICNP) now includes the categories domain and kingdom. For purpose valid publication their names under ICNP, we consider here two known domains, ‘ Bacteria ’ Archaea ’, as well a number taxa suitable for rank kingdom, based on previous phylogenetic taxonomic studies. It is proposed to subdivide into kingdoms Bacillati , Fusobacteriati Pseudomonadati Thermotogati . This arrangement reflects contemporary hypotheses proposals cell wall structure, including ‘diderms’ vs. ‘monoderms’, Gracilicutes Firmicutes Negibacteria Unibacteria Hydrobacteria Terrabacteria Hydrobacterida Terrabacterida ’. include Methanobacteriati Nanobdellati Thermoproteati reflecting division Euryarchaeota ‘DPANN superphylum’ ‘TACK superphylum’.

Language: Английский

Citations

14
Engineering Biocatalysts for the C−H Activation of Fatty Acids by Ancestral Sequence Reconstruction** DOI Creative Commons
Bethan S. Jones,

Connie M. Ross,

Gabriel Foley

et al.

Angewandte Chemie International Edition, Journal Year: 2024, Volume and Issue: 63(18)

Published: Jan. 1, 2024

Abstract Selective, one‐step C−H activation of fatty acids from biomass is an attractive concept in sustainable chemistry. Biocatalysis has shown promise for generating high‐value hydroxy acids, but to date enzyme discovery relied on laborious screening and produced limited hits, which predominantly oxidise the subterminal positions acids. Herein we show that ancestral sequence reconstruction (ASR) effective tool explore sequence‐activity landscape a family multidomain, self‐sufficient P450 monooxygenases. We resurrected 11 catalytically active CYP116B ancestors, each with unique regioselectivity fingerprint varied older ancestors mid‐chain lineage leading extant, P450‐TT. In lineages extant enzymes thermophiles, thermostability increased forms, as expected if thermophily had arisen de novo. Our studies ASR can be applied multidomain develop active, monooxygenases regioselective biocatalysts acid hydroxylation.

Language: Английский

Citations

9
The link between ancient microbial fluoride resistance mechanisms and bioengineering organofluorine degradation or synthesis DOI Creative Commons
Randy B Stockbridge,

Lawrence P. Wackett

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

Published: May 30, 2024

Abstract Fluorinated organic chemicals, such as per- and polyfluorinated alkyl substances (PFAS) fluorinated pesticides, are both broadly useful unusually long-lived. To combat problems related to the accumulation of these compounds, microbial PFAS organofluorine degradation biosynthesis less-fluorinated replacement chemicals under intense study. Both efforts undermined by substantial toxicity fluoride, an anion that powerfully inhibits metabolism. Microorganisms have contended with environmental mineral fluoride over evolutionary time, evolving a suite detoxification mechanisms. In this perspective, we synthesize emerging ideas on defluorination/fluorination resistance mechanisms identify best approaches for bioengineering new degrading making compounds.

Language: Английский

Citations

9
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

Citations

8