Systematic evaluation of C. elegans lincRNAs with CRISPR knockout mutants

AbstractAnimals are often not growing at the maximum rate, but can compensate for a bad start of life by further increasing growth rate. While this compensatory growth is widespread, its direct fitness consequences are seldom investigated and its genetic basis is unknown. We investigated the genetic regulation, as well as fitness and lifespan consequences of compensatory growth in response to temperature, using C. elegans knockout of the thermo-sensitive TRP ion channel TRPA-1, involved in temperature recognition. We exposed juvenile worms to cold, normal or warm temperatures in order to delay or speed up development. After returning to normal temperature, we found that wild-type worms where early development was delayed, expressed compensatory growth and catched up in size, while juvenile exposure to warm temperatures expressed slowed-down growth and small size. Compensatory growth also altered the reproductive schedule towards early reproduction, so that rate-sensitive individual fitness increased even though total reproduction was unaffected. Surprisingly, no lifespan cost of compensatory growth was found. In contrast, juvenile temperature did not induce compensatory or slowed-down growth in the trpa-1 knockout mutants, and consequently did not affect fitness. We show that temperature-induced compensatory growth in C. elegans is regulated by the trpa-1 and can increase fitness.

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Assessment of community efforts to advance computational prediction of protein-protein interactions

10.1101/2021.09.22.461292 ◽

2021 ◽

Author(s):

Xu-Wen Wang ◽

Lorenzo Madeddu ◽

Kerstin Spirohn ◽

Leonardo Martini ◽

Adriano Fazzone ◽

...

Keyword(s):

Protein Interactions ◽

Molecular Mechanisms ◽

Computational Prediction ◽

Superior Performance ◽

Systematic Evaluation ◽

Human Interactome ◽

C Elegans ◽

Protein Protein Interaction ◽

Human Ppis ◽

Underlying Network

AbstractComprehensive insights from the human protein-protein interaction (PPI) network, known as the human interactome, can provide important insights into the molecular mechanisms of complex biological processes and diseases. Despite the remarkable experimental efforts undertaken to date to determine the structure of the human interactome, many PPIs remain unmapped. Computational approaches, especially network-based methods, can facilitate the identification of new PPIs. Many such approaches have been proposed. However, a systematic evaluation of existing network-based methods in predicting PPIs is still lacking. Here, we report community efforts initiated by the International Network Medicine Consortium to benchmark the ability of 24 representative network-based methods to predict PPIs across five different interactomes, including a synthetic interactome generated by the duplication-mutation-complementation model, and the interactomes of four different organisms: A. thaliana, C. elegans, S. cerevisiae, and H. sapiens. We selected the top-seven methods through a computational validation on the human interactome. We next experimentally validated their top-500 predicted PPIs (in total 3,276 predicted PPIs) using the yeast two-hybrid assay, finding 1,177 new human PPIs (involving 633 proteins). Our results indicate that task-tailored similarity-based methods, which leverage the underlying network characteristics of PPIs, show superior performance over other general link prediction methods. Through experimental validation, we confirmed that the top-ranking methods show promising performance externally. For example, from the top 500 PPIs predicted by an advanced similarity-base method [MPS(B&T)], 430 were successfully tested by Y2H with 376 testing positive, yielding a precision of 87.4%. These results establish advanced similarity-based methods as powerful tools for the prediction of human PPIs.

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Two populations of cytoplasmic dynein contribute to spindle positioning in C. elegans embryos

The Journal of Cell Biology ◽

10.1083/jcb.201607038 ◽

2017 ◽

Vol 216 (9) ◽

pp. 2777-2793 ◽

Cited By ~ 21

Author(s):

Ruben Schmidt ◽

Lars-Eric Fielmich ◽

Ilya Grigoriev ◽

Eugene A. Katrukha ◽

Anna Akhmanova ◽

...

Keyword(s):

Cytoplasmic Dynein ◽

Force Generation ◽

Cell Cortex ◽

Animal Cells ◽

Spindle Positioning ◽

C Elegans ◽

Knockout Mutants ◽

Pulling Forces ◽

Endogenous Proteins ◽

Pulling Force

The position of the mitotic spindle is tightly controlled in animal cells as it determines the plane and orientation of cell division. Contacts between cytoplasmic dynein and astral microtubules (MTs) at the cell cortex generate pulling forces that position the spindle. An evolutionarily conserved Gα-GPR-1/2Pins/LGN–LIN-5Mud/NuMA cortical complex interacts with dynein and is required for pulling force generation, but the dynamics of this process remain unclear. In this study, by fluorescently labeling endogenous proteins in Caenorhabditis elegans embryos, we show that dynein exists in two distinct cortical populations. One population directly depends on LIN-5, whereas the other is concentrated at MT plus ends and depends on end-binding (EB) proteins. Knockout mutants lacking all EBs are viable and fertile and display normal pulling forces and spindle positioning. However, EB protein–dependent dynein plus end tracking was found to contribute to force generation in embryos with a partially perturbed dynein function, indicating the existence of two mechanisms that together create a highly robust force-generating system.

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A novel assay for the detection of anthelmintic activity mediated by cuticular damage to nematodes: validation onCaenorhabditis elegansexposed to cysteine proteinases

Parasitology ◽

10.1017/s0031182016002353 ◽

2017 ◽

Vol 144 (5) ◽

pp. 583-593 ◽

Cited By ~ 3

Author(s):

A. M. PHIRI ◽

D. I. DE POMERAI ◽

D. J. BUTTLE ◽

J. M. BEHNKE

Keyword(s):

Colorimetric Assay ◽

Anthelmintic Activity ◽

Neutral Red ◽

Cysteine Proteinases ◽

C Elegans ◽

Viable Cells ◽

Knockout Mutants ◽

Red Dye ◽

Hydrolysis Of

SUMMARYPlant cysteine proteinases (CPs) fromCarica papayakill parasitic and free-living nematodesin vitroby hydrolysis of the worm cuticle, a mechanism that is different to all commercially available synthetic anthelmintics. We have developed a cheap and effective, rapid-throughputCaenorhabditis elegans-based assay for screening plant CP extracts for anthelmintic activity targeting cuticular integrity. The assay exploits colorimetric methodology for assessment of cuticular damage, and is based on the ability of viable cells to incorporate and bind Neutral red dye within lysosomes and to release the dye when damaged. Living worms are pre-stained with the dye, exposed to CPs and then leakage of the dye through the damaged cuticle is quantified by spectrophotometry. In contrast to motility assays and semi-subjective interpretation of microscopical images, this colorimetric assay is independent of observer bias. Our assay was applied to a series ofC. elegans busmutant strains with leaky cuticles and to cystatin knockout mutants. At ambient temperature and over 0.5–24 h, bothbusmutants and the cystatin knockouts were highly susceptible to CPs, whereas wild-type Bristol N2 worms were essentially unstained by Neutral red and unaffected by CPs, providing validation for the utility of this assay.

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Image Analysis of Intramembrane Particles in Freeze-Fractured Biomembranes Using Computer Simulation Techniques

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100114694 ◽

1975 ◽

Vol 33 ◽

pp. 214-215

Author(s):

D.J. Benefiel ◽

R.S. Weinstein

Keyword(s):

Membrane Proteins ◽

Freeze Fracture ◽

Integral Membrane Proteins ◽

Systematic Evaluation ◽

Intramembrane Particles ◽

Modeling Methods ◽

Simulation Techniques ◽

Freeze Fracture Electron Microscopy ◽

Fracture Electron ◽

Computer Simulation Techniques

Intramembrane particles (IMP or MAP) are components of most biomembranes. They are visualized by freeze-fracture electron microscopy, and they probably represent replicas of integral membrane proteins. The presence of MAP in biomembranes has been extensively investigated but their detailed ultrastructure has been largely ignored. In this study, we have attempted to lay groundwork for a systematic evaluation of MAP ultrastructure. Using mathematical modeling methods, we have simulated the electron optical appearances of idealized globular proteins as they might be expected to appear in replicas under defined conditions. By comparing these images with the apearances of MAPs in replicas, we have attempted to evaluate dimensional and shape distortions that may be introduced by the freeze-fracture technique and further to deduce the actual shapes of integral membrane proteins from their freezefracture images.

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The glycomes of Caenorhabditis elegans and other model organisms

Biochemical Society Symposium ◽

10.1042/bss0690117 ◽

2002 ◽

Vol 69 ◽

pp. 117-134 ◽

Cited By ~ 47

Author(s):

Stuart M. Haslam ◽

David Gems ◽

Howard R. Morris ◽

Anne Dell

Keyword(s):

Caenorhabditis Elegans ◽

Current Knowledge ◽

Structural Data ◽

Model Organisms ◽

Entire Genome ◽

C Elegans ◽

The Face ◽

Area Of Concern ◽

Nematode Worm

There is no doubt that the immense amount of information that is being generated by the initial sequencing and secondary interrogation of various genomes will change the face of glycobiological research. However, a major area of concern is that detailed structural knowledge of the ultimate products of genes that are identified as being involved in glycoconjugate biosynthesis is still limited. This is illustrated clearly by the nematode worm Caenorhabditis elegans, which was the first multicellular organism to have its entire genome sequenced. To date, only limited structural data on the glycosylated molecules of this organism have been reported. Our laboratory is addressing this problem by performing detailed MS structural characterization of the N-linked glycans of C. elegans; high-mannose structures dominate, with only minor amounts of complex-type structures. Novel, highly fucosylated truncated structures are also present which are difucosylated on the proximal N-acetylglucosamine of the chitobiose core as well as containing unusual Fucα1–2Gal1–2Man as peripheral structures. The implications of these results in terms of the identification of ligands for genomically predicted lectins and potential glycosyltransferases are discussed in this chapter. Current knowledge on the glycomes of other model organisms such as Dictyostelium discoideum, Saccharomyces cerevisiae and Drosophila melanogaster is also discussed briefly.

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How do histone modifications contribute to transgenerational epigenetic inheritance in C. elegans?

Biochemical Society Transactions ◽

10.1042/bst20190944 ◽

2020 ◽

Vol 48 (3) ◽

pp. 1019-1034 ◽

Cited By ~ 1

Author(s):

Rachel M. Woodhouse ◽

Alyson Ashe

Keyword(s):

Histone Modifications ◽

Molecular Mechanisms ◽

Epigenetic Inheritance ◽

Nematode Caenorhabditis Elegans ◽

Histone Methyltransferases ◽

Transgenerational Epigenetic Inheritance ◽

C Elegans ◽

Recent Developments ◽

Gene Regulatory

Gene regulatory information can be inherited between generations in a phenomenon termed transgenerational epigenetic inheritance (TEI). While examples of TEI in many animals accumulate, the nematode Caenorhabditis elegans has proven particularly useful in investigating the underlying molecular mechanisms of this phenomenon. In C. elegans and other animals, the modification of histone proteins has emerged as a potential carrier and effector of transgenerational epigenetic information. In this review, we explore the contribution of histone modifications to TEI in C. elegans. We describe the role of repressive histone marks, histone methyltransferases, and associated chromatin factors in heritable gene silencing, and discuss recent developments and unanswered questions in how these factors integrate with other known TEI mechanisms. We also review the transgenerational effects of the manipulation of histone modifications on germline health and longevity.

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Centrosome Aurora A gradient ensures single polarity axis in C. elegans embryos

Biochemical Society Transactions ◽

10.1042/bst20200298 ◽

2020 ◽

Vol 48 (3) ◽

pp. 1243-1253 ◽

Cited By ~ 1

Author(s):

Sukriti Kapoor ◽

Sachin Kotak

Keyword(s):

Symmetry Breaking ◽

Cell Fate ◽

Cell Cortex ◽

Axis Formation ◽

Aurora A Kinase ◽

Aurora A ◽

C Elegans ◽

Cell Embryo ◽

Polarity Establishment

Cellular asymmetries are vital for generating cell fate diversity during development and in stem cells. In the newly fertilized Caenorhabditis elegans embryo, centrosomes are responsible for polarity establishment, i.e. anterior–posterior body axis formation. The signal for polarity originates from the centrosomes and is transmitted to the cell cortex, where it disassembles the actomyosin network. This event leads to symmetry breaking and the establishment of distinct domains of evolutionarily conserved PAR proteins. However, the identity of an essential component that localizes to the centrosomes and promotes symmetry breaking was unknown. Recent work has uncovered that the loss of Aurora A kinase (AIR-1 in C. elegans and hereafter referred to as Aurora A) in the one-cell embryo disrupts stereotypical actomyosin-based cortical flows that occur at the time of polarity establishment. This misregulation of actomyosin flow dynamics results in the occurrence of two polarity axes. Notably, the role of Aurora A in ensuring a single polarity axis is independent of its well-established function in centrosome maturation. The mechanism by which Aurora A directs symmetry breaking is likely through direct regulation of Rho-dependent contractility. In this mini-review, we will discuss the unconventional role of Aurora A kinase in polarity establishment in C. elegans embryos and propose a refined model of centrosome-dependent symmetry breaking.

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