scholarly journals KMT5C encodes robust heterochromatin retention and liquid-like behavior using limited sequence features

2021 ◽  
Author(s):  
Hilmar Strickfaden ◽  
Kristal Missiaen ◽  
Justin W Knechtel ◽  
Michael J Hendzel ◽  
D Alan Underhill
Keyword(s):  
Liquid Droplet ◽  
Strongly Correlated ◽  
Protein Retention ◽  
Sequence Features ◽  
Multiple Strategies ◽  
Lysine Methyltransferase ◽  
Membrane Bound ◽  
High Connectivity ◽  
Linear Motifs ◽  
Limited Sequence

Cells use multiple strategies to compartmentalize functions through a combination of membrane-bound and membraneless organelles. The latter represent complex assemblies of biomolecules that coalesce into a dense phase through low affinity, multivalent interactions and undergo rapid exchange with the surrounding dilute phase. We describe a liquid-like state for the lysine methyltransferase KMT5C characterized by diffusion within heterochromatin condensates but lacking appreciable nucleoplasmic exchange. Retention was strongly correlated with reduction of condensate surface area, suggesting formation of a liquid droplet with high connectivity. This behavior mapped to a discrete domain whose activity was dependent on multiple short linear motifs. Moreover, it was strikingly resilient to marked phylogenetic differences or targeted changes in intrinsic disorder, charge, sequence, and architecture. Collectively, these findings show that a limited number of sequence features can dominantly encode multivalency, localization, and dynamic behavior within heterochromatin condensates to confer protein retention without progression to a gel or solid.

scholarly journals Phylogenomics-guided discovery of a novel conserved cassette of short linear motifs in BubR1 essential for the spindle checkpoint

Open Biology ◽  
2016 ◽  
Vol 6 (12) ◽  
pp. 160315 ◽  
Author(s):  
Eelco Tromer ◽  
Debora Bade ◽  
Berend Snel ◽  
Geert J. P. L. Kops
Keyword(s):  
Spindle Assembly Checkpoint ◽  
De Novo ◽  
Mitotic Cell ◽  
Ancestral Sequence ◽  
Gene Duplications ◽  
Functional Protein ◽  
Guided Discovery ◽  
Sequence Features ◽  
Spindle Microtubules ◽  
Linear Motifs

The spindle assembly checkpoint (SAC) maintains genomic integrity by preventing progression of mitotic cell division until all chromosomes are stably attached to spindle microtubules. The SAC critically relies on the paralogues Bub1 and BubR1/Mad3, which integrate kinetochore–spindle attachment status with generation of the anaphase inhibitory complex MCC. We previously reported on the widespread occurrences of independent gene duplications of an ancestral ‘MadBub’ gene in eukaryotic evolution and the striking parallel subfunctionalization that lead to loss of kinase function in BubR1/Mad3-like paralogues. Here, we present an elaborate subfunctionalization analysis of the Bub1/BubR1 gene family and perform de novo sequence discovery in a comparative phylogenomics framework to trace the distribution of ancestral sequence features to extant paralogues throughout the eukaryotic tree of life. We show that known ancestral sequence features are consistently retained in the same functional paralogue: GLEBS/CMI/CDII/kinase in the Bub1-like and KEN1/KEN2/D-Box in the BubR1/Mad3-like. The recently described ABBA motif can be found in either or both paralogues. We however discovered two additional ABBA motifs that flank KEN2. This cassette of ABBA1-KEN2-ABBA2 forms a strictly conserved module in all ancestral and BubR1/Mad3-like proteins, suggestive of a specific and crucial SAC function. Indeed, deletion of the ABBA motifs in human BUBR1 abrogates the SAC and affects APC/C–Cdc20 interactions. Our detailed comparative genomics analyses thus enabled discovery of a conserved cassette of motifs essential for the SAC and shows how this approach can be used to uncover hitherto unrecognized functional protein features.

scholarly journals Quantitative Principles ofcis-translational control by general mRNA sequence features in eukaryotes

2019 ◽  
Author(s):  
Jingyi Jessica Li ◽  
Guo-Liang Chew ◽  
Mark D. Biggin
Keyword(s):  
Translational Control ◽  
Rna Structure ◽  
Open Reading Frames ◽  
Sequence Length ◽  
Strongly Correlated ◽  
Protein Coding ◽  
Biochemical Processes ◽  
Sequence Features ◽  
Upstream Open Reading Frames ◽  
Control Translation

ABSTRACTBACKGROUNDGeneral translationalcis-elements are present in the mRNAs of all genes and affect the recruitment, assembly, and progress of preinitiation complexes and the ribosome under many physiological states. These elements are: mRNA folding, upstream open reading frames, specific nucleotides flanking the initiating AUG codon, protein coding sequence length, and codon usage. The quantitative contributions of these sequence features and how and why they coordinate together to control translation rates are not well understood.RESULTSHere we show that these sequence features specify 42%–81% of the variance in translation rates inS.cerevisiae, S.pombe, Arabidopsis thaliana, M.musculus, andH.Sapiens. We establish that control by RNA secondary structure is chiefly mediated by highly folded 25–60 nucleotide segments within mRNA 5’ regions; that changes in tri-nucleotide frequencies between highly and poorly translated 5’ regions are correlated between all species; and that control by distinct biochemical processes is extensively correlated as is regulation by a single process acting in different parts of the same mRNA.CONCLUSIONSOur work shows that the general features control a much larger fraction of the variance in translation rates than previously realized. We provide a more detailed and accurate understanding of the aspects of RNA structure that direct translation in diverse eukaryotes. In addition, we note that the strongly correlated regulation between and withincis-control features will cause more even densities of translational complexes along each mRNA and therefore more efficient use of the translation machinery by the cell.

scholarly journals Seasonal shifts in the vertical distribution of fish in a shallow coastal area

2016 ◽  
Vol 73 (9) ◽  
pp. 2278-2287 ◽  
Author(s):  
Noora Mustamäki ◽  
Henri Jokinen ◽  
Matias Scheinin ◽  
Erik Bonsdorff ◽  
Johanna Mattila
Keyword(s):  
Vertical Distribution ◽  
Sampling Design ◽  
Juvenile Fish ◽  
Trophic Levels ◽  
Strongly Correlated ◽  
High Connectivity ◽  
The Vertical Distribution ◽  
Spatial Resource Partitioning ◽  
Distribution Of Fish ◽  
Shallow Coastal Area

Abstract Depth structures aquatic habitats, creating substantial differences in the species composition of underwater communities even at small intervals. Those communities also undergo considerable cyclic variation annually. In this study, we surveyed variation in the vertical distribution of fish in a shallow (20 m) coastal basin in the northern Baltic Sea during the ice-free period from May to October. The waters were strongly mixed throughout the season and only transient signs of stratification were observed. As production shifted towards higher trophic levels over summer, with sequential biomass peaks in zooplankton and juvenile fish, the vertical distribution of the entire fish assemblage became increasingly even. The results suggest that spatial resource partitioning can be strongly correlated with seasonal productivity cycles even in physically uniform environments with high connectivity. Further, the results stress the importance of sampling design (seasonal and vertical coverage) of fish studies in shallow coastal areas.

scholarly journals Effect of Ser-129 Phosphorylation on Interaction of α-Synuclein with Synaptic and Cellular Membranes

2011 ◽  
Vol 286 (41) ◽  
pp. 35863-35873 ◽  
Author(s):  
Naomi P. Visanji ◽  
Sabine Wislet-Gendebien ◽  
Loren W. Oschipok ◽  
Gang Zhang ◽  
Isabelle Aubert ◽  
...  
Keyword(s):  
Proteasome Inhibitor ◽  
Membrane Binding ◽  
Lewy Bodies ◽  
Neural Precursor Cells ◽  
Synaptic Membranes ◽  
Membrane Association ◽  
Synaptosomal Membranes ◽  
Multiple Strategies ◽  
Membrane Bound ◽  
Deficient Mice

In the healthy brain, less than 5% of α-synuclein (α-syn) is phosphorylated at serine 129 (Ser(P)-129). However, within Parkinson disease (PD) Lewy bodies, 89% of α-syn is Ser(P)-129. The effects of Ser(P)-129 modification on α-syn distribution and solubility are poorly understood. As α-syn normally exists in both membrane-bound and cytosolic compartments, we examined the binding and dissociation of Ser(P)-129 α-syn and analyzed the effects of manipulating Ser(P)-129 levels on α-syn membrane interactions using synaptosomal membranes and neural precursor cells from α-syn-deficient mice or transgenic mice expressing human α-syn. We first evaluated the recovery of the Ser(P)-129 epitope following either α-syn membrane binding or dissociation. We demonstrate a rapid turnover of Ser(P)-129 during both binding to and dissociation from synaptic membranes. Although the membrane binding of WT α-syn was insensitive to modulation of Ser(P)-129 levels by multiple strategies (the use of phosphomimic S129D and nonphosphorylated S129A α-syn mutants; by enzymatic dephosphorylation of Ser(P)-129 or proteasome inhibitor-induced elevation in Ser(P)-129; or by inhibition or stable overexpression of PLK2), PD mutant Ser(P)-129 α-syn showed a preferential membrane association compared with WT Ser(P)-129 α-syn. Collectively, these data suggest that phosphorylation at Ser-129 is dynamic and that the subcellular distribution of α-syn bearing PD-linked mutations, A30P or A53T, is influenced by the phosphorylation state of Ser-129.

scholarly journals Membraneless organelles formed by liquid-liquid phase separation increase bacterial fitness

2021 ◽  
Author(s):  
Xin Jin ◽  
Ji-Eun Lee ◽  
Charley Schaefer ◽  
Xinwei Luo ◽  
Adam JM Wollman ◽  
...  
Keyword(s):  
Phase Separation ◽  
Liquid Phase ◽  
Liquid Droplet ◽  
Quantitative Agreement ◽  
Liquid Phase Separation ◽  
Cell Processes ◽  
Bacterial Fitness ◽  
Membrane Bound ◽  
Multiple Species ◽  
Liquid Liquid Phase Separation

Liquid-liquid phase separation is emerging as a crucial phenomenon in several fundamental cell processes. A range of eukaryotic systems exhibit liquid condensates. However, their function in bacteria, which in general lack membrane-bound compartments, remains less clear. Here, we used high-resolution optical microscopy to observe single bacterial aggresomes, nanostructured intracellular assemblies of proteins, to undercover their role in cell stress. We find that proteins inside aggresomes are mobile and undergo dynamic turnover, consistent with a liquid state. Our observations are in quantitative agreement with phase-separated liquid droplet formation driven by interacting proteins under thermal equilibrium that nucleate following diffusive collisions in the cytoplasm. We have discovered aggresomes in multiple species of bacteria, and show that these emergent, metastable liquid-structured protein assemblies increase bacterial fitness by enabling cells to tolerate environmental stresses.

scholarly journals KMT5C displays robust retention and liquid-like behavior in phase separated heterochromatin

2019 ◽  
Author(s):  
Hilmar Strickfaden ◽  
Kristal Missiaen ◽  
Michael J. Hendzel ◽  
D. Alan Underhill
Keyword(s):  
Phase Separation ◽  
Spatial Constraint ◽  
Heterochromatin Protein ◽  
Spatial Control ◽  
Conserved Sequence ◽  
Lysine Methyltransferase ◽  
General Phase ◽  
Membrane Bound ◽  
Specific Activities ◽  
Protein Mecp2

AbstractThe pericentromere exists as a distinct chromatin compartment that is thought to form by a process of phase separation. This reflects the ability of the heterochromatin protein CBX5 (aka HP1α) to form liquid condensates that encapsulate pericentromeres.1,2 In general, phase separation compartmentalizes specific activities within the cell, but unlike membrane-bound organelles, their contents rapidly exchange with their surroundings.3 Here, we describe a novel state for the lysine methyltransferase KMT5C where it diffuses within condensates of pericentromeric heterochromatin but undergoes strikingly limited nucleoplasmic exchange, revealing a barrier to exit similar to that of biological membranes. This liquid-like behavior maps to a discrete protein segment with a small number of conserved sequence features and containing separable determinants for localization and retention that cooperate to confer strict spatial control. Accordingly, loss of KMT5C retention led to aberrant spreading of its catalytic product (H4K20me3) throughout the nucleus. We further found that KMT5C retention was reversible in response to chromatin state, which differed markedly for CBX5 and the methyl-CpG binding protein MeCP2, revealing considerable plasticity in the control of these phase separated assemblies. Our results establish that KMT5C represents a precedent in the biological phase separation4 continuum that confers robust spatial constraint of a protein and its catalytic activity without progression to a gel or solid.

Two Distinct Types of Microfilaments in the Cytoplasm of Human Adenohypophysial Cells

1973 ◽  
Vol 31 ◽  
pp. 668-669
Author(s):  
E. Horvath ◽  
K. Kovacs ◽  
I. E. Stratmann ◽  
C. Ezrin
Keyword(s):  
Pituitary Tumors ◽  
Average Diameter ◽  
Anterior Lobe ◽  
Uranyl Acetate ◽  
Type I ◽  
Breast Cancer Patients ◽  
Human Pituitary ◽  
Severe Diabetes ◽  
Pituitary Glands ◽  
Membrane Bound

Surgically removed human pituitary glands as well as pituitary tumors fixed in glutaraldehyde, postfixed in osmium tetroxide, embedded in epon resin, stained with uranyl acetate and lead citrate have been investigated by electron microscopy in order to correlate ultrastructure with functional activity. In the course of this study two distinct types of microfilaments have been identified in the cytoplasm of adenohypophysiocytes.Type I microfilaments (Fig. 1) were found in the cytoplasm of anterior lobe cells of five female subjects with disseminated mammary cancer and two patients with severe diabetes mellitus. The breast cancer patients were treated pre-operatively for various periods of time with different doses of oxysteroids. The microfilaments had an average diameter of JO A, formed parallel bundles, were scattered irregularly in the cytoplasm and were frequently located in the perikaryon. They were not membrane-bound and failed to show any periodicity.

Intranuclear Crystals in Regenerating Canine Kidneys

1973 ◽  
Vol 31 ◽  
pp. 412-413
Author(s):  
D.G. Osborne ◽  
L.J. McCormack ◽  
M.O. Magnusson ◽  
W.S. Kiser
Keyword(s):  
Epithelial Cell ◽  
Epithelial Cells ◽  
Tubular Epithelial Cell ◽  
Tubular Epithelial Cells ◽  
Cell Nuclei ◽  
Crystalline Structures ◽  
Small Crystals ◽  
Membrane Bound

During a project in which regenerative changes were studied in autotransplanted canine kidneys, intranuclear crystals were seen in a small number of tubular epithelial cells. These crystalline structures were seen in the control specimens and also in regenerating specimens; the main differences being in size and number of them. The control specimens showed a few tubular epithelial cell nuclei almost completely occupied by large crystals that were not membrane bound. Subsequent follow-up biopsies of the same kidneys contained similar intranuclear crystals but of a much smaller size. Some of these nuclei contained several small crystals. The small crystals occurred at one week following transplantation and were seen even four weeks following transplantation. As time passed, the small crystals appeared to fuse to form larger crystals.

Membrane-bound vesicles associated with the microvilli in the midgut of the freshwater microcrustacean, Daphnia magna

1983 ◽  
Vol 41 ◽  
pp. 480-481
Author(s):  
Patricia L. Jansma
Keyword(s):  
Daphnia Magna ◽  
Intestinal Epithelial Cells ◽  
Uranyl Acetate ◽  
Intestinal Epithelial ◽  
Chlamydomonas Reinhardii ◽  
Thin Sections ◽  
Saturated Water ◽  
Cacodylate Buffer ◽  
Membrane Bound ◽  
Ethanol Series

The presence of the membrane bound vesicles or blebs on the intestinal epithelial cells has been demonstrated in a variety of vertebrates such as chicks, piglets, hamsters, and humans. The only invertebrates shown to have these microvillar blebs are two species of f1ies. While investigating the digestive processes of the freshwater microcrustacean, Daphnia magna, the presence of these microvillar blebs was noticed.Daphnia magna fed in a suspension of axenically grown green alga, Chlamydomonas reinhardii for one hour were narcotized with CO2 saturated water. The intestinal tracts were excised in 2% glutaraldehyde in 0.2 M cacodyl ate buffer and then placed in fresh 2% glutaraldehyde for one hour. After rinsing in 0.1 M cacodylate buffer, the sample was postfixed in 2% OsO4, dehydrated with a graded ethanol series, infiltrated and embedded with Epon-Araldite. Thin sections were stained with uranyl acetate and Reynolds lead citrate before viewing with the Philips EM 200.

Analysis of the Anterior Secretory Cells of Onchidohs Muricata (Nudibranchia)

1981 ◽  
Vol 39 ◽  
pp. 614-615
Author(s):  
Roy Skidmore
Keyword(s):  
Endoplasmic Reticulum ◽  
Secretory Granules ◽  
Golgi Body ◽  
The Body ◽  
Secretory Cells ◽  
Secretory Vesicles ◽  
High Magnification ◽  
Large Numbers ◽  
Membrane Bound ◽  
Sole Of The Foot

The long-necked secretory cells in Onchidoris muricata are distributed in the anterior sole of the foot. These cells are interspersed among ciliated columnar and conical cells as well as short-necked secretory gland cells. The long-necked cells contribute a significant amount of mucoid materials to the slime on which the nudibranch travels. The body of these cells is found in the subepidermal tissues. A long process extends across the basal lamina and in between cells of the epidermis to the surface of the foot. The secretory granules travel along the process and their contents are expelled by exocytosis at the foot surface.The contents of the cell body include the nucleus, some endoplasmic reticulum, and an extensive Golgi body with large numbers of secretory vesicles (Fig. 1). The secretory vesicles are membrane bound and contain a fibrillar matrix. At high magnification the similarity of the contents in the Golgi saccules and the secretory vesicles becomes apparent (Fig. 2).

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