Analysis of biological noise in the flagellar length control system

Bauer, Diana; Ishikawa, Hiroaki; Wemmer, Kimberly A.; Hendel, Nathan L.; Kondev, Jané; Marshall, Wallace F.

doi:10.1016/j.isci.2021.102354

Cited by 26 publications

(42 citation statements)

References 86 publications

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“…CC-1690 and CC-5325 also had some differences in cilia length and swimming speed ( Figure 10 ). CC-5325 had longer cilia in TAP medium than CC-1690, consistent with the increased cell volume of CC-5325 in TAP as compared to CC-1690 ( Figure 1 ), as ciliary length scales with cell size [ 79 ]. CC-5325 had slower swimming speed in M-N medium than CC-1690, which may be related to additional influences by positive gravitaxis (downward swimming in response to gravity), as we observed that CC-5325 gravitaxed and settled faster than CC-1690 in both TAP and M-N medium.…”

Section: Discussionmentioning

confidence: 55%

Comparative Phenotyping of Two Commonly Used Chlamydomonas reinhardtii Background Strains: CC-1690 (21gr) and CC-5325 (The CLiP Mutant Library Background)

Pazouki

Nguyen

Jacobshagen

et al. 2022

Plants

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The unicellular green alga Chlamydomonas reinhardtii is an excellent model organism to investigate many essential cellular processes in photosynthetic eukaryotes. Two commonly used background strains of Chlamydomonas are CC-1690 and CC-5325. CC-1690, also called 21gr, has been used for the Chlamydomonas genome project and several transcriptome analyses. CC-5325 is the background strain for the Chlamydomonas Library Project (CLiP). Photosynthetic performance in CC-5325 has not been evaluated in comparison with CC-1690. Additionally, CC-5325 is often considered to be cell-wall deficient, although detailed analysis is missing. The circadian rhythms in CC-5325 are also unclear. To fill these knowledge gaps and facilitate the use of the CLiP mutant library for various screens, we performed phenotypic comparisons between CC-1690 and CC-5325. Our results showed that CC-5325 grew faster heterotrophically in dark and equally well in mixotrophic liquid medium as compared to CC-1690. CC-5325 had lower photosynthetic efficiency and was more heat-sensitive than CC-1690. Furthermore, CC-5325 had an intact cell wall which had comparable integrity to that in CC-1690 but appeared to have reduced thickness. Additionally, CC-5325 could perform phototaxis, but could not maintain a sustained circadian rhythm of phototaxis as CC1690 did. Finally, in comparison to CC-1690, CC-5325 had longer cilia in the medium with acetate but slower swimming speed in the medium without nitrogen and acetate. Our results will be useful for researchers in the Chlamydomonas community to choose suitable background strains for mutant analysis and employ the CLiP mutant library for genome-wide mutant screens under appropriate conditions, especially in the areas of photosynthesis, thermotolerance, cell wall, and circadian rhythms.

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Section: Discussionmentioning

confidence: 55%

Comparative Phenotyping of Two Commonly Used Chlamydomonas reinhardtii Background Strains: CC-1690 (21gr) and CC-5325 (The CLiP Mutant Library Background)

Pazouki

Nguyen

Jacobshagen

et al. 2022

Plants

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“…Further, related strategies may be used to control the growth of radial microtubule arrays that reach the cell periphery (27,28), and may explain the scaling relationships observed between flagellar length and cell length (29) and between contractile ring diameter and cell diameter (30).…”

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confidence: 99%

Scaling of subcellular actin structures with cell length through decelerated growth

McInally

Kondev

Goode

2021

eLife

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How cells tune the size of their subcellular parts to scale with cell size is a fundamental question in cell biology. Until now, most studies on the size control of organelles and other subcellular structures have focused on scaling relationships with cell volume, which can be explained by limiting pool mechanisms. Here, we uncover a distinct scaling relationship with cell length rather than volume, revealed by mathematical modeling and quantitative imaging of yeast actin cables. The extension rate of cables decelerates as they approach the rear of the cell, until cable length matches cell length. Further, the deceleration rate scales with cell length. These observations are quantitatively explained by a 'balance-point' model, which stands in contrast to the limiting pool mechanisms and that senses the linear dimensions of the cell.

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“…As described in the introduction, a scale invariant protein gradient is useful to a cell that is in need of determining position within the cell relative to its linear dimensions, such as in the case of patterning in development [1]. Another possible use for such a gradient could be in controlling the self-assembly of linear structures such as actin cables and flagella, which are precisely scaled to the linear dimensions of the cell [29], [30], [31]. For example, a recent study of actin cables in yeast found that when cells were mutated to grow abnormally large, the actin cables assembled to a length that was proportional to the cell radius [32].…”

Section: Discussionmentioning

confidence: 99%

How to Assemble a Scale-Invariant Gradient

Datta

Ghosh

Kondev

2021

Preprint

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Intracellular protein gradients serve a variety of functions, such as the establishment of cell polarity and to provide positional information for gene expression in developing embryos. Given that cell size in a population can vary considerably, for the protein gradients to work properly they often have to be scaled to the size of the cell. Here we examine a model of protein gradient formation within a cell that relies on cytoplasmic diffusion and cortical transport of proteins toward a cell pole. We show that the shape of the protein gradient is determined solely by the cell geometry. Furthermore, we show that the length scale over which the protein concentration in the gradient varies is determined by the linear dimensions of the cell, independent of the diffusion constant or the transport speed. This gradient provides scale-invariant positional information within a cell, which can be used for assembly of intracellular structures whose size is scaled to the linear dimensions of the cell, as was recently reported for the cytokinetic ring and actin cables in budding yeast cells.

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Analysis of biological noise in the flagellar length control system

Cited by 26 publications

References 86 publications

Comparative Phenotyping of Two Commonly Used Chlamydomonas reinhardtii Background Strains: CC-1690 (21gr) and CC-5325 (The CLiP Mutant Library Background)

Comparative Phenotyping of Two Commonly Used Chlamydomonas reinhardtii Background Strains: CC-1690 (21gr) and CC-5325 (The CLiP Mutant Library Background)

Scaling of subcellular actin structures with cell length through decelerated growth

How to Assemble a Scale-Invariant Gradient

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