Automated model building and protein identification in cryo-EM maps

Nature, Journal Year: 2024, Volume and Issue: 628(8007), P. 450 - 457

Published: Feb. 26, 2024

Interpreting electron cryo-microscopy (cryo-EM) maps with atomic models requires high levels of expertise and labour-intensive manual intervention in three-dimensional computer graphics programs

Language: Английский

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Automated model building and protein identification in cryo-EM maps

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

Published: May 16, 2023

Interpreting electron cryo-microscopy (cryo-EM) maps with atomic models requires high levels of expertise and labour-intensive manual intervention. We present ModelAngelo, a machine-learning approach for automated model building in cryo-EM maps. By combining information from the map protein sequence structure single graph neural network, ModelAngelo builds proteins that are similar quality as those generated by human experts. For nucleotides, backbones accuracy humans. using its predicted amino acid probabilities each residue hidden Markov searches, outperforms experts identification unknown sequences. will thus remove bottlenecks increase objectivity determination.

Language: Английский

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The pyrenoid: the eukaryotic CO2-concentrating organelle

The Plant Cell, Journal Year: 2023, Volume and Issue: 35(9), P. 3236 - 3259

Published: June 4, 2023

The pyrenoid is a phase-separated organelle that enhances photosynthetic carbon assimilation in most eukaryotic algae and the land plant hornwort lineage. Pyrenoids mediate approximately one-third of global CO2 fixation, engineering into C3 crops predicted to boost uptake increase yields. enhance activity CO2-fixing enzyme Rubisco by supplying it with concentrated CO2. All pyrenoids have dense matrix associated thylakoid membranes are thought supply Many also surrounded polysaccharide structures may slow leakage. Phylogenetic analysis morphological diversity support convergent evolutionary origin for pyrenoids. Most molecular understanding comes from model green alga Chlamydomonas (Chlamydomonas reinhardtii). exhibits multiple liquid-like behaviors, including internal mixing, division fission, dissolution condensation response environmental cues during cell cycle. Pyrenoid assembly function induced availability light, although transcriptional regulators been identified, posttranslational regulation remains be characterized. Here, we summarize current knowledge function, structure, components, dynamic extrapolate other species.

Language: Английский

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The structure, function, and evolution of plant centromeres

Genome Research, Journal Year: 2024, Volume and Issue: 34(2), P. 161 - 178

Published: Feb. 1, 2024

Centromeres are essential regions of eukaryotic chromosomes responsible for the formation kinetochore complexes, which connect to spindle microtubules during cell division. Notably, although centromeres maintain a conserved function in chromosome segregation, underlying DNA sequences diverse both within and between species predominantly repetitive nature. The repeat content includes high-copy tandem repeats (satellites), and/or specific families transposons. functional region centromere is defined by loading histone 3 variant (CENH3), nucleates shows dynamic regulation. In many plants, composed satellite arrays that densely methylated invaded centrophilic retrotransposons. some cases, retrotransposons become sites CENH3 loading. We review structure plant centromeres, including monocentric, holocentric, metapolycentric architectures, vary number distribution attachment along chromosomes. discuss how variation can drive genome elimination early divisions embryogenesis. epigenetic state may influence identity evolutionary models seek explain paradoxically rapid change observed across species, potential roles recombination. outline putative modes selection could act as well role driving cycles evolution. Although our primary focus on genomes, we draw comparisons with animal fungal derive eukaryote-wide perspective function.

Language: Английский

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Extensive remodeling during Chlamydomonas reinhardtii zygote maturation leads to highly resistant zygospores

The Plant Journal, Journal Year: 2025, Volume and Issue: 121(3)

Published: Feb. 1, 2025

SUMMARY The unicellular soil alga Chlamydomonas reinhardtii forms diploid zygotes during its sexual cycle. process of a zygote maturing into highly resistant zygospore remains poorly understood despite importance for survival under adverse environmental conditions. Here we describe the detailed timeline morphological and physiological changes maturation in darkness on ammonium‐free Tris‐acetate‐phosphate agar plates. formation multilayered cell wall is primarily responsible increase size first few days after formation. Desiccation freezing tolerance also develop period 3–7 days. Photosynthetic respiratory activity decrease to reach minimal levels 7–10 days, accompanied by partial dedifferentiation chloroplast that includes chlorophyll degradation followed possible disappearance pyrenoid. In contrast decreasing concentrations most carotenoids formation, ketocarotenoids can be detected 3 their accumulation completed 10 Furthermore, degrades large proportion starch enriches oligosaccharides may serve as osmoprotectants. storage lipid triacylglycerol accumulated at expense thylakoid membrane lipids, which mirrors conversion metabolically active dormant spore metabolic level. Taken together, multifaceted yields mature zygospores ~ weeks. This work sheds light complete time course remodeling photosynthetically eukaryotic dormant, spore.

Language: Английский

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The synthetic future of algal genomes

Cell Genomics, Journal Year: 2024, Volume and Issue: 4(3), P. 100505 - 100505

Published: Feb. 22, 2024

Algae are diverse organisms with significant biotechnological potential for resource circularity. Taking inspiration from fermentative microbes, engineering algal genomes holds promise to broadly expand their application ranges. Advances in genome sequencing improvements DNA synthesis and delivery techniques enabling customized molecular tool development confer advanced traits algae. Efforts redesign rebuild entire create fit-for-purpose currently being explored heterotrophic prokaryotes eukaryotic microbes could also be applied photosynthetic Future will enhance yields of native products permit the expression complex biochemical pathways produce novel metabolites sustainable inputs. We present a historical perspective on advances algae, discuss requisite genetic enable optimization, take whole-genome efforts other systems, candidate species context these goals.

Language: Английский

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Exchange or Eliminate: The Secrets of Algal-Bacterial Relationships

Plants, Journal Year: 2024, Volume and Issue: 13(6), P. 829 - 829

Published: March 13, 2024

Algae and bacteria have co-occurred coevolved in common habitats for hundreds of millions years, fostering specific associations interactions such as mutualism or antagonism. These are shaped through exchanges primary secondary metabolites provided by one the partners. Metabolites, N-sources vitamins, can be beneficial to partner they may assimilated chemotaxis towards producing these metabolites. Other metabolites, especially many natural products synthesized bacteria, act toxins damage kill partner. For instance, green microalga Chlamydomonas reinhardtii establishes a mutualistic partnership with Methylobacterium, stark contrast its antagonistic relationship toxin Pseudomonas protegens. In other cases, coccolithophore haptophyte alga Phaeobacter bacterium, same bacterium even subject both processes, depending on secreted bacterial algal Some also influence morphology micronutrients, is observed some macroalgae. This review focuses algal-bacterial micro- macroalgal models from marine, freshwater, terrestrial environments summarizes advances field. It highlights effects temperature it presently known.

Language: Английский

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Extensive structural rearrangement of intraflagellar transport trains underpins bidirectional cargo transport

Cell, Journal Year: 2024, Volume and Issue: 187(17), P. 4621 - 4636.e18

Published: July 26, 2024

Bidirectional transport in cilia is carried out by polymers of the IFTA and IFTB protein complexes, called anterograde retrograde intraflagellar (IFT) trains. Anterograde trains deliver cargoes from cell to cilium tip, then convert into for cargo export. We set understand how IFT complexes can perform these two directly opposing roles before after conversion. use cryoelectron tomography situ cross-linking mass spectrometry determine structure compare it with known The train a 2-fold symmetric polymer organized around central thread complexes. conclude that anterograde-to-retrograde remodeling involves global rearrangements IFTA/B requires complete disassembly train. Finally, we describe conformational changes cargo-binding sites facilitate unidirectional bidirectional system.

Language: Английский

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Chlamydomonas reinhardtii, Volvox carteri and related green algae accumulate ketocarotenoids not in vegetative cells but in zygospores

The Plant Journal, Journal Year: 2025, Volume and Issue: 121(3)

Published: Feb. 1, 2025

Zygospores of green alga such as Chlamydomonas reinhardtii, Volvox carteri or Dunaliella salina display a bright orange color indicative carotenoids, yet there have been no reports on their pigment composition. The genomes these algae contain genes for homologs the β-carotene ketolase (BKT) from well-known astaxanthin producer Haematococcus pluvialis, that were assumed to be pseudogenes, because none species has reported accumulate other ketocarotenoids. Here, we show C. reinhardtii and V. synthesize ketocarotenoids specifically in zygospores. Contrary vegetative aplanospores H. major ketocarotenoid zygospores is not but 4-ketolutein. Moreover, maturing are synthesized de novo carotenoids photosynthetic apparatus liberated by massive breakdown thylakoid membranes. In line with this conclusion, incubation at 9°C instead 22°C resulted reduced only low amounts ketocarotenoids, while accumulation storage lipids was less affected. Furthermore, full-length BKT catalyze ketolation both α-carotene lutein carotenogenic bacteria. We also detected putative various known suggesting zygospore-specific common among Chlamydomonadales. Our observation together sheds light physiology largely unexplored algal life stage crucial survival propagation.

Language: Английский

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Leaky ribosomal scanning enables tunable translation of bicistronic ORFs in green algae

Proceedings of the National Academy of Sciences, Journal Year: 2025, Volume and Issue: 122(9)

Published: Feb. 26, 2025

Advances in sequencing technology have unveiled examples of nucleus-encoded polycistrons, once considered rare. Exclusively polycistronic transcripts are prevalent green algae, although the mechanism by which multiple polypeptides translated from a single transcript is unknown. Here, we used bioinformatic and vivo mutational analyses to evaluate competing mechanistic models for translation bicistronic mRNAs algae. High-confidence manually curated datasets loci two divergent Chlamydomonas reinhardtii Auxenochlorella protothecoides , revealed preference weak Kozak-like sequences ORF 1 an underrepresentation potential initiation codons before 2 start codon, suitable conditions leaky ribosome scanning allow translation. We analysis A. test mechanism. In manipulation sequence codon altered reporter expression at 2, with weaker enhancing stronger one diminishing it. A synthetic dual demonstrated inversely adjustable activity fluorescent protein expressed luciferase depending on strength sequence. Our findings demonstrate that ORFs algal consistent episodic 2. This work has implications functionality upstream open reading frames (uORFs) found across eukaryotic genomes transgene biology applications.

Language: Английский

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