Non-model model organisms

Russell, J. J.; Theriot, Julie A.; Sood, Pranidhi; Marshall, Wallace F.; Landweber, Laura F.; Fritz‐Laylin, Lillian K.; Polka, Jessica; Oliferenko, Snezhana; Gerbich, Therese M.; Gladfelter, Amy; Umen, James G.; Bezanilla, Magdalena; Lancaster, Madeline A.; He, Shuonan; Gibson, Matthew C.; Goldstein, Bob; Tanaka, Elly M.; Hu, Chi-Kuo; Brunet, Anne

doi:10.1186/s12915-017-0391-5

Cited by 199 publications

(168 citation statements)

References 310 publications

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“…The fission yeasts Schizosaccharomyces pombe and Schizosaccharomyces japonicus show remarkable differences in fundamental membrane-centered processes such as establishment of polarity and mitotic nuclear envelope (NE) remodeling [1, 2]. The different strategies of managing the NE have been linked to the distinct regulation of lipid synthesis during the cell cycle in the two species [3, 4].…”

Section: Resultsmentioning

confidence: 99%

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Delineating the rules for structural adaptation of membrane-associated proteins to evolutionary changes in membrane lipidome

Makarova

Péter

Balogh

et al. 2019

Preprint

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Membrane function is fundamental to life. Each species explores membrane lipid diversity within a genetically predefined range of possibilities. How membrane lipid composition in turn defines the functional space available for evolution of membranecentered processes remains largely unknown. We address this fundamental question using related fission yeasts Schizosaccharomyces pombe and Schizosaccharomyces japonicus. We show that unlike S. pombe that generates membranes where both glycerophospholipid acyl tails are predominantly 16-18 carbons long, S. japonicus synthesizes unusual 'asymmetrical' glycerophospholipids where the tails differ in length by 6-8 carbons. This results in stiffer bilayers with distinct lipid packing properties. Retroengineered S. pombe synthesizing the S. japonicus-type phospholipids exhibits unfolded protein response and downregulates secretion. Importantly, our protein sequence comparisons and domain swap experiments indicate that transmembrane helices co-evolve with membranes, suggesting that, on the evolutionary scale, changes in membrane lipid composition may necessitate extensive adaptation of the membrane-associated proteome. Results and DiscussionThe fission yeasts Schizosaccharomyces pombe and Schizosaccharomyces japonicus show remarkable differences in fundamental membrane-centered processes such as establishment of polarity and mitotic nuclear envelope (NE) remodeling [1, 2]. The different strategies of managing the NE have been linked to the distinct regulation of lipid synthesis during the cell cycle in the two species [3, 4].To analyze membrane lipid compositions of the two sister species, we performed shotgun ESI-MS/MS analysis of total cellular lipid extracts (Supplemental Table 1).3

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Section: Resultsmentioning

confidence: 99%

“…For growth rate measurements, cells were grown in EMM (unless otherwise stated) overnight, diluted to OD 595 0.2 and supplemented with cerulenin (10µg/ml in DMSO) and/or FAs conjugated with BSA based on recommendations described in [1]. FA stock (5 mM) was prepared in 50% ethanol heated to 70°C.…”

Section: Cell Growth and Survival Measurementsmentioning

confidence: 99%

Delineating the rules for structural adaptation of membrane-associated proteins to evolutionary changes in membrane lipidome

Makarova

Péter

Balogh

et al. 2019

Preprint

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“…The improved accessibility of sequencing technology makes it easier to access genomic data, and contributes significantly to molecular biology in non-classical model organisms (Russell et al, 2017). Long read assemblies are especially useful in this regard in complex large eukaryotic genomes, typically with numerous non-random features such as highly repetitive sequences and polyploidy (Kono, Nakamura, Ohtoshi, Pedrazzoli Moran, et al, 2019;Kono, Nakamura, Ohtoshi, Tomita, Numata, et al, 2019).…”

Section: Us E C a S E: Hi G Hly Repe Titive S Pider S Ilk G Ene Smentioning

confidence: 99%

Nanopore sequencing: Review of potential applications in functional genomics

2019

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Molecular biology has been led by various measurement technologies, and increased throughput has developed omics analysis. The development of massively parallel sequencing technology has enabled access to fundamental molecular data and revealed genomic and transcriptomic signatures. Nanopore sequencers have driven such evolution to the next stage. Oxford Nanopore Technologies Inc. provides a new type of single molecule sequencer using protein nanopore that realizes direct sequencing without DNA synthesizing or amplification. This nanopore sequencer can sequence an ultra‐long read limited by the input nucleotide length, or can determine DNA/RNA modifications. Recently, many fields such as medicine, epidemiology, ecology, and education have benefited from this technology. In this review, we explain the features and functions of the nanopore sequencer, introduce various situations where it has been used as a critical technology, and expected future applications.

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“…As the number of species with emerging interest for research increases (Russell et al., 2017; Sanchez Alvarado, 2018), identifying a system advantageous to answer specific questions is more critical than ever. As laid out by Steve Austad in 1997, choosing a research organism involves tradeoffs between factors such as realism , repeatability of results , and feasibility (Austad, 1997; Figure 1).…”

Section: Research Organisms For Agingmentioning

confidence: 99%

The African turquoise killifish: A research organism to study vertebrate aging and diapause

Brunet²

2018

Aging Cell

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SummaryThe African turquoise killifish has recently gained significant traction as a new research organism in the aging field. Our understanding of aging has strongly benefited from canonical research organisms—yeast, C. elegans, Drosophila, zebrafish, and mice. Many characteristics that are essential to understand aging—for example, the adaptive immune system or the hypothalamo‐pituitary axis—are only present in vertebrates (zebrafish and mice). However, zebrafish and mice live more than 3 years and their relatively long lifespans are not compatible with high‐throughput studies. Therefore, the turquoise killifish, a vertebrate with a naturally compressed lifespan of only 4–6 months, fills an essential gap to understand aging. With a recently developed genomic and genetic toolkit, the turquoise killifish not only provides practical advantages for lifespan and longitudinal experiments, but also allows more systematic characterizations of the interplay between genetics and environment during vertebrate aging. Interestingly, the turquoise killifish can also enter a long‐term dormant state during development called diapause. Killifish embryos in diapause already have some organs and tissues, and they can last in this state for years, exhibiting exceptional resistance to stress and to damages due to the passage of time. Understanding the diapause state could give new insights into strategies to prevent the damage caused by aging and to better preserve organs, tissues, and cells. Thus, the African turquoise killifish brings two interesting aspects to the aging field—a compressed lifespan and a long‐term resistant diapause state, both of which should spark new discoveries in the field.

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Non-model model organisms

Cited by 199 publications

References 310 publications

Delineating the rules for structural adaptation of membrane-associated proteins to evolutionary changes in membrane lipidome

Delineating the rules for structural adaptation of membrane-associated proteins to evolutionary changes in membrane lipidome

Nanopore sequencing: Review of potential applications in functional genomics

The African turquoise killifish: A research organism to study vertebrate aging and diapause

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