scholarly journals Archaeal cell biology: diverse functions of tubulin-like cytoskeletal proteins at the cell envelope

2018 ◽  
Vol 2 (4) ◽  
pp. 547-559 ◽  
Author(s):  
Yan Liao ◽  
Solenne Ithurbide ◽  
Roshali T. de Silva ◽  
Susanne Erdmann ◽  
Iain G. Duggin
Keyword(s):  
Cell Biology ◽  
Shape Control ◽  
Cell Envelope ◽  
Light And Electron Microscopy ◽  
Halophilic Archaea ◽  
Cytoskeletal Proteins ◽  
Model Organisms ◽  
Full Spectrum ◽  
Peptidoglycan Cell Wall ◽  
Domains Of Life

The tubulin superfamily of cytoskeletal proteins is widespread in all three domains of life — Archaea, Bacteria and Eukarya. Tubulins build the microtubules of the eukaryotic cytoskeleton, whereas members of the homologous FtsZ family construct the division ring in prokaryotes and some eukaryotic organelles. Their functions are relatively poorly understood in archaea, yet these microbes contain a remarkable diversity of tubulin superfamily proteins, including FtsZ for division, a newly described major family called CetZ that is involved in archaeal cell shape control, and several other divergent families of unclear function that are implicated in a variety of cell envelope-remodelling contexts. Archaeal model organisms, particularly halophilic archaea such as Haloferax volcanii, have sufficiently developed genetic tools and we show why their large, flattened cells that are capable of controlled differentiation are also well suited to cell biological investigations by live-cell high-resolution light and electron microscopy. As most archaea only have a glycoprotein lattice S-layer, rather than a peptidoglycan cell wall like bacteria, the activity of the tubulin-like cytoskeletal proteins at the cell envelope is expected to vary significantly, and may involve direct membrane remodelling or directed synthesis or insertion of the S-layer protein subunits. Further studies of archaeal cell biology will provide fresh insight into the evolution of cells and the principles in common to their fundamental activities across the full spectrum of cellular life.

Cryo-fixation and associated developments in transmission electron microscopy: a cool future for nematology

Nematology ◽  
2016 ◽  
Vol 18 (1) ◽  
pp. 1-14 ◽  
Author(s):  
Wim Bert ◽  
Dieter Slos ◽  
Olivier Leroux ◽  
Myriam Claeys
Keyword(s):  
Electron Microscopy ◽  
Cell Biology ◽  
Electron Tomography ◽  
Light And Electron Microscopy ◽  
Three Dimensional ◽  
Freeze Substitution ◽  
Model Organisms ◽  
Fixation Method ◽  
Dimensional Reconstruction ◽  
Fixation Techniques

At present, the importance of sample preparation equipment for electron microscopy represents the driving force behind major breakthroughs in microscopy and cell biology. In this paper we present an introduction to the most commonly used cryo-fixation techniques, with special attention paid towards high-pressure freezing followed by freeze substitution. Techniques associated with cryo-fixation, such as immunolocalisation, cryo-sectioning, and correlative light and electron microscopy, are also highlighted. For studies that do not require high resolution, high quality results, or the immediate arrest of certain processes, conventional methods will provide answers to many questions. For some applications, such as immunocytochemistry, three-dimensional reconstruction of serial sections or electron tomography, improved preservation of the ultrastructure is required. This review of nematode cryo-fixation highlights that cryo-fixation not only results in a superior preservation of fine structural details, but also underlines the fact that some observations based on results solely obtained through conventional fixation approaches were either incorrect, or otherwise had severe limitations. Although the use of cryo-fixation has hitherto been largely restricted to model organisms, the advantages of cryo-fixation are sufficiently self-evident that we must conclude that the cryo-fixation method is highly likely to become the standard for nematode fixation in the near future.

scholarly journals Transfection of choanoflagellates illuminates their cell biology and the ancestry of animal septins

2018 ◽  
Vol 29 (25) ◽  
pp. 3026-3038 ◽  
Author(s):  
David S. Booth ◽  
Heather Szmidt-Middleton ◽  
Nicole King
Keyword(s):  
Cell Biology ◽  
Fluorescent Protein ◽  
Animal Cell ◽  
Single Cells ◽  
Dna Delivery ◽  
Cytoskeletal Proteins ◽  
Model Organisms ◽  
Protein Markers ◽  
Foreign Genes ◽  
Salpingoeca Rosetta

As the closest living relatives of animals, choanoflagellates offer unique insights into animal origins and core mechanisms underlying animal cell biology. However, unlike traditional model organisms, such as yeast, flies, and worms, choanoflagellates have been refractory to DNA delivery methods for expressing foreign genes. Here we report a robust method for expressing transgenes in the choanoflagellate Salpingoeca rosetta, overcoming barriers that have previously hampered DNA delivery and expression. To demonstrate how this method accelerates the study of S. rosetta cell biology, we engineered a panel of fluorescent protein markers that illuminate key features of choanoflagellate cells. We then investigated the localization of choanoflagellate septins, a family of GTP-binding cytoskeletal proteins that are hypothesized to regulate multicellular rosette development in S. rosetta. Fluorescently tagged septins localized to the basal poles of S. rosetta single cells and rosettes in a pattern resembling septin localization in animal epithelia. The establishment of transfection in S. rosetta and its application to the study of septins represent critical advances in the use of S. rosetta as an experimental model for investigating choanoflagellate cell biology, core mechanisms underlying animal cell biology, and the origin of animals.

scholarly journals Choanoflagellate transfection illuminates their cell biology and the ancestry of animal septins

2018 ◽  
Author(s):  
David S. Booth ◽  
Heather Szmidt-Middleton ◽  
Nicole King
Keyword(s):  
Cell Biology ◽  
Fluorescent Protein ◽  
Animal Cell ◽  
Single Cells ◽  
Dna Delivery ◽  
Cytoskeletal Proteins ◽  
Model Organisms ◽  
Protein Markers ◽  
Foreign Genes ◽  
Salpingoeca Rosetta

ABSTRACTAs the closest living relatives of animals, choanoflagellates offer unique insights into animal origins and core mechanisms underlying animal cell biology. However, unlike traditional model organisms, such as yeast, flies and worms, choanoflagellates have been refractory to DNA delivery methods for expressing foreign genes. Here we report the establishment of a robust method for expressing transgenes in the choanoflagellate Salpingoeca rosetta, overcoming barriers that have previously hampered DNA delivery and expression. To demonstrate how this method accelerates the study of S. rosetta cell biology, we engineered a panel of fluorescent protein markers that illuminate key features of choanoflagellate cells. We then investigated the localization of choanoflagellate septins, a family of GTP-binding cytoskeletal proteins that are hypothesized to regulate the multicellular rosette development in S. rosetta. Fluorescently tagged septins localized to the basal pole of S. rosetta single cells and rosettes in a pattern resembling septin localization in animal epithelia. The establishment of transfection in S. rosetta and its application to the study of septins represent critical advances in the growth of S. rosetta as an experimental model for investigating choanoflagellate cell biology, core mechanisms underlying animal cell biology, and the origin of animals.

scholarly journals Publisher Correction: Genetic tool development in marine protists: emerging model organisms for experimental cell biology

2020 ◽  
Vol 17 (5) ◽  
pp. 551-551
Author(s):  
Drahomíra Faktorová ◽  
R. Ellen R. Nisbet ◽  
José A. Fernández Robledo ◽  
Elena Casacuberta ◽  
Lisa Sudek ◽  
...  
Keyword(s):  
Cell Biology ◽  
Model Organisms ◽  
Tool Development ◽  
Experimental Cell ◽  
Genetic Tool ◽  
Marine Protists

scholarly journals Cellular dynamics of EMT: lessons from live in vivo imaging of embryonic development

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Jeffrey D. Amack
Keyword(s):  
Extracellular Matrix ◽  
Embryonic Development ◽  
In Vivo Imaging ◽  
Cytoskeletal Proteins ◽  
Cell Junctions ◽  
Model Organisms ◽  
Cellular Dynamics ◽  
Mesenchymal Transition ◽  
Cell Cell

AbstractEpithelial-mesenchymal transition (EMT) refers to a process in which epithelial cells lose apical-basal polarity and loosen cell–cell junctions to take on mesenchymal cell morphologies and invasive properties that facilitate migration through extracellular matrix. EMT—and the reverse mesenchymal-epithelial transition (MET)—are evolutionarily conserved processes that are used throughout embryonic development to drive tissue morphogenesis. During adult life, EMT is activated to close wounds after injury, but also can be used by cancers to promote metastasis. EMT is controlled by several mechanisms that depend on context. In response to cell–cell signaling and/or interactions with the local environment, cells undergoing EMT make rapid changes in kinase and adaptor proteins, adhesion and extracellular matrix molecules, and gene expression. Many of these changes modulate localization, activity, or expression of cytoskeletal proteins that mediate cell shape changes and cell motility. Since cellular changes during EMT are highly dynamic and context-dependent, it is ideal to analyze this process in situ in living organisms. Embryonic development of model organisms is amenable to live time-lapse microscopy, which provides an opportunity to watch EMT as it happens. Here, with a focus on functions of the actin cytoskeleton, I review recent examples of how live in vivo imaging of embryonic development has led to new insights into mechanisms of EMT. At the same time, I highlight specific developmental processes in model embryos—gastrulation in fly and mouse embryos, and neural crest cell development in zebrafish and frog embryos—that provide in vivo platforms for visualizing cellular dynamics during EMT. In addition, I introduce Kupffer’s vesicle in the zebrafish embryo as a new model system to investigate EMT and MET. I discuss how these systems have provided insights into the dynamics of adherens junction remodeling, planar cell polarity signaling, cadherin functions, and cytoskeletal organization during EMT, which are not only important for understanding development, but also cancer progression. These findings shed light on mechanisms of actin cytoskeletal dynamics during EMT, and feature live in vivo imaging strategies that can be exploited in future work to identify new mechanisms of EMT and MET.

scholarly journals Phyletic distribution and diversification of the Phage Shock Protein stress response system in bacteria and archaea

2021 ◽  
Author(s):  
Philipp F. Popp ◽  
Vadim M. Gumerov ◽  
Ekaterina P. Andrianova ◽  
Lisa Bewersdorf ◽  
Thorsten Mascher ◽  
...  
Keyword(s):  
Stress Response ◽  
Large Scale ◽  
Cell Envelope ◽  
Model Organisms ◽  
Microbial World ◽  
Natural Classification ◽  
Response System ◽  
Core Proteins ◽  
Envelope Stress

AbstractThe bacterial cell envelope is an essential structure that protects the cell from environmental threats, while simultaneously serving as communication interface and diffusion barrier. Therefore, maintaining cell envelope integrity is of vital importance for all microorganisms. Not surprisingly, evolution has shaped conserved protection networks that connect stress perception, transmembrane signal transduction and mediation of cellular responses upon cell envelope stress. The phage shock protein (PSP) stress response is one of such conserved protection networks. Most of the knowledge about the Psp response comes from studies in the Gram-negative model bacterium, Escherichia coli where the Psp system consists of several well-defined protein components. Homologous systems were identified in representatives of Proteobacteria, Actinobacteria, and Firmicutes; however, the Psp system distribution in the microbial world remains largely unknown. By carrying out a large-scale, unbiased comparative genomics analysis, we found components of the Psp system in many bacterial and archaeal phyla and demonstrated that the PSP system deviates dramatically from the proteobacterial prototype. Two of its core proteins, PspA and PspC, have been integrated in various (often phylum-specifically) conserved protein networks during evolution. Based on protein sequence and gene neighborhood analyses of pspA and pspC homologs, we built a natural classification system of PSP networks in bacteria and archaea. We performed a comprehensive in vivo protein interaction screen for the PSP network newly identified in the Gram-positive model organism Bacillus subtilis and found a strong interconnected PSP response system, illustrating the validity of our approach. Our study highlights the diversity of PSP organization and function across many bacterial and archaeal phyla and will serve as foundation for future studies of this envelope stress response beyond model organisms.

scholarly journals Siblings or doppelgängers? Deciphering the evolution of structured cis-regulatory RNAs beyond homology

2020 ◽  
Vol 48 (5) ◽  
pp. 1941-1951
Author(s):  
Elizabeth C. Gray ◽  
Daniel M. Beringer ◽  
Michelle M. Meyer
Keyword(s):  
Functional Diversity ◽  
Sequence Similarity ◽  
Functional Validation ◽  
Rna Sequences ◽  
Full Spectrum ◽  
Regulatory Molecule ◽  
Mrna Transcripts ◽  
Domains Of Life ◽  
Regulatory Rnas

Structured cis-regulatory RNAs have evolved across all domains of life, highlighting the utility and plasticity of RNA as a regulatory molecule. Homologous RNA sequences and structures often have similar functions, but homology may also be deceiving. The challenges that derive from trying to assign function to structure and vice versa are not trivial. Bacterial riboswitches, viral and eukaryotic IRESes, CITEs, and 3′ UTR elements employ an array of mechanisms to exert their effects. Bioinformatic searches coupled with biochemical and functional validation have elucidated some shared and many unique ways cis-regulators are employed in mRNA transcripts. As cis-regulatory RNAs are resolved in greater detail, it is increasingly apparent that shared homology can mask the full spectrum of mRNA cis-regulator functional diversity. Furthermore, similar functions may be obscured by lack of obvious sequence similarity. Thus looking beyond homology is crucial for furthering our understanding of RNA-based regulation.

Positional Correlative Anatomy of Invertebrate Model Organisms Increases Efficiency of TEM Data Production

2014 ◽  
Vol 20 (5) ◽  
pp. 1392-1403 ◽  
Author(s):  
Irina Kolotuev
Keyword(s):  
Developmental Biology ◽  
Cell Biology ◽  
Sampling Rate ◽  
Unmet Need ◽  
Region Of Interest ◽  
Model Organisms ◽  
Data Generation ◽  
Step Method ◽  
Efficient Data ◽  
Research Questions

AbstractTransmission electron microscopy (TEM) is an important tool for studies in cell biology, and is essential to address research questions from bacteria to animals. Recent technological innovations have advanced the entire field of TEM, yet classical techniques still prevail for most present-day studies. Indeed, the majority of cell and developmental biology studies that use TEM do not require cutting-edge methodologies, but rather fast and efficient data generation. Although access to state-of-the-art equipment is frequently problematic, standard TEM microscopes are typically available, even in modest research facilities. However, a major unmet need in standard TEM is the ability to quickly prepare and orient a sample to identify a region of interest. Here, I provide a detailed step-by-step method for a positional correlative anatomy approach to flat-embedded samples. These modifications make the TEM preparation and analytic procedures faster and more straightforward, supporting a higher sampling rate. To illustrate the modified procedures, I provide numerous examples addressing research questions in Caenorhabditis elegans and Drosophila. This method can be equally applied to address questions of cell and developmental biology in other small multicellular model organisms.

Growth and Division of the Peptidoglycan Matrix

2021 ◽  
Vol 75 (1) ◽  
Author(s):  
Patricia D.A. Rohs ◽  
Thomas G. Bernhardt
Keyword(s):  
Cell Wall ◽  
Bacterial Infections ◽  
Model Organisms ◽  
Annual Review ◽  
Publication Date ◽  
Drug Resistant ◽  
Peptidoglycan Cell Wall ◽  
Integral Role ◽  
Osmotic Lysis ◽  
Peptidoglycan Layer

Most bacteria are surrounded by a peptidoglycan cell wall that defines their shape and protects them from osmotic lysis. The expansion and division of this structure therefore plays an integral role in bacterial growth and division. Additionally, the biogenesis of the peptidoglycan layer is the target of many of our most effective antibiotics. Thus, a better understanding of how the cell wall is built will enable the development of new therapies to combat the rise of drug-resistant bacterial infections. This review covers recent advances in defining the mechanisms involved in assembling the peptidoglycan layer with an emphasis on discoveries related to the function and regulation of the cell elongation and division machineries in the model organisms Escherichia coli and Bacillus subtilis. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

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