Lipid Cell Biology: A Focus on Lipids in Cell Division

Cells depend on hugely diverse lipidomes for many functions. The actions and structural integrity of the plasma membrane and most organelles also critically depend on membranes and their lipid components. Despite the biological importance of lipids, our understanding of lipid engagement, especially the roles of lipid hydrophobic alkyl side chains, in key cellular processes is still developing. Emerging research has begun to dissect the importance of lipids in intricate events such as cell division. This review discusses how these structurally diverse biomolecules are spatially and temporally regulated during cell division, with a focus on cytokinesis. We analyze how lipids facilitate changes in cellular morphology during division and how they participate in key signaling events. We identify which cytokinesis proteins are associated with membranes, suggesting lipid interactions. More broadly, we highlight key unaddressed questions in lipid cell biology and techniques, including mass spectrometry, advanced imaging, and chemical biology, which will help us gain insights into the functional roles of lipids.

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Live cell imaging of the hyperthermophilic archaeon Sulfolobus acidocaldarius identifies complementary roles for two ESCRTIII homologues in ensuring a robust and symmetric cell division

10.1101/2020.02.18.953042 ◽

2020 ◽

Cited By ~ 2

Author(s):

Andre Arashiro Pulschen ◽

Delyan R. Mutavchiev ◽

Kim Nadine Sebastian ◽

Jacques Roubinet ◽

Marc Roubinet ◽

...

Keyword(s):

Cell Division ◽

Cell Biology ◽

Live Cell Imaging ◽

Cell Imaging ◽

Halophilic Archaea ◽

Live Cell ◽

Tight Coupling ◽

Dna Compaction ◽

Cellular Processes ◽

Daughter Cells

Live-cell imaging has revolutionized our understanding of dynamic cellular processes in bacteria and eukaryotes. While similar techniques have recently been applied to the study of halophilic archaea, our ability to explore the cell biology of thermophilic archaea is limited, due to the technical challenges of imaging at high temperatures. Here, we report the construction of the Sulfoscope, a heated chamber that enables live-cell imaging on an inverted fluorescent microscope. Using this system combined with thermostable fluorescent probes, we were able to image Sulfolobus cells as they divide, revealing a tight coupling between changes in DNA compaction, segregation and cytokinesis. By imaging deletion mutants, we observe important differences in the function of the two ESCRTIII proteins recently implicated in cytokinesis. The loss of CdvB1 compromises cell division, causing occasional division failures and fusion of the two daughter cells, whereas the deletion of cdvB2 leads to a profound loss of division symmetry, generating daughter cells that vary widely in size and eventually generating ghost cells. These data indicate that DNA separation and cytokinesis are coordinated in Sulfolobus, as is the case in eukaryotes, and that two contractile ESCRTIII polymers perform distinct roles to ensure that Sulfolobus cells undergo a robust and symmetrical division. Taken together, the Sulfoscope has shown to provide a controlled high temperature environment, in which cell biology of Sulfolobus can be studied in unprecedent details.

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Inhibiting IFT dynein with ciliobrevin in C. elegans chemosensory cilia

10.1101/531848 ◽

2019 ◽

Author(s):

Jona Mijalkovic ◽

Erwin J.G. Peterman

Keyword(s):

Cell Division ◽

Small Molecule ◽

Intracellular Transport ◽

Structural Integrity ◽

Cytoplasmic Dynein ◽

Treatment Results ◽

C Elegans ◽

Cellular Processes ◽

Transport Velocity ◽

High Fraction

AbstractCytoplasmic dyneins play a role in a myriad of cellular processes, such as retrograde intracellular transport and cell division. Small-molecule cytoplasmic dynein antagonists, ciliobrevins, have recently been developed as tools to acutely probe cytoplasmic dynein function. Although widely used to investigate cytoplasmic dynein 1, far fewer studies explore the effect of ciliobrevin on cytoplasmic dynein 2 or IFT dynein. Here, we use ciliobrevin A to partially disrupt IFT dynein in the chemosensory cilia of living C. elegans. Acute, low-concentration ciliobrevin treatment results in shortening of cilia and reduction of transport velocity in both directions. After longer exposure to ciliobrevin, we find concentration-dependent motor accumulations and axonemal deformations. We propose that maintenance of ciliary length requires a high fraction of active IFT-dynein motors, while structural integrity can be preserved by only a few active motors.

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Cell division protein FtsZ: from structure and mechanism to antibiotic target

Future Microbiology ◽

10.2217/fmb-2019-0348 ◽

2020 ◽

Vol 15 (9) ◽

pp. 801-831 ◽

Cited By ~ 1

Author(s):

Nadine Silber ◽

Cruz L Matos de Opitz ◽

Christian Mayer ◽

Peter Sass

Keyword(s):

Cell Division ◽

Bacterial Cell ◽

Cell Biology ◽

Bacterial Infections ◽

Structural Integrity ◽

Antimicrobial Activities ◽

Bacterial Cell Division ◽

Antibiotic Target ◽

Resistance Breaking ◽

Cell Division Protein

Antimicrobial resistance to virtually all clinically applied antibiotic classes severely limits the available options to treat bacterial infections. Hence, there is an urgent need to develop and evaluate new antibiotics and targets with resistance-breaking properties. Bacterial cell division has emerged as a new antibiotic target pathway to counteract multidrug-resistant pathogens. New approaches in antibiotic discovery and bacterial cell biology helped to identify compounds that either directly interact with the major cell division protein FtsZ, thereby perturbing the function and dynamics of the cell division machinery, or affect the structural integrity of FtsZ by inducing its degradation. The impressive antimicrobial activities and resistance-breaking properties of certain compounds validate the inhibition of bacterial cell division as a promising strategy for antibiotic intervention.

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Specific protein–lipid interactions in membrane proteins

Biochemical Society Transactions ◽

10.1042/bst0330938 ◽

2005 ◽

Vol 33 (5) ◽

pp. 938-942 ◽

Cited By ~ 56

Author(s):

C. Hunte

Keyword(s):

Membrane Proteins ◽

Membrane Protein ◽

Structural Integrity ◽

Protein Structures ◽

Specific Protein ◽

Lipid Binding ◽

Functional Roles ◽

Lipid Interactions ◽

Head Groups ◽

Lipid Species

Many membrane proteins selectively bind defined lipid species. This specificity has an impact on correct insertion, folding, structural integrity and full functionality of the protein. How are these different tasks achieved? Recent advances in structural research of membrane proteins provide new information about specific protein–lipid interactions. Tightly bound lipids in membrane protein structures are described and general principles of the binding interactions are deduced. Lipid binding is stabilized by multiple non-covalent interactions from protein residues to lipid head groups and hydrophobic tails. Distinct lipid-binding motifs have been identified for lipids with defined head groups in membrane protein structures. The stabilizing interactions differ between the electropositive and electronegative membrane sides. The importance of lipid binding for vertical positioning and tight integration of proteins in the membrane, for assembly and stabilization of oligomeric and multisubunit complexes, for supercomplexes, as well as for functional roles are pointed out.

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Functional Roles of Bromodomain Proteins in Cancer

Cancers ◽

10.3390/cancers13143606 ◽

2021 ◽

Vol 13 (14) ◽

pp. 3606

Author(s):

Samuel P. Boyson ◽

Cong Gao ◽

Kathleen Quinn ◽

Joseph Boyd ◽

Hana Paculova ◽

...

Keyword(s):

Open Chromatin ◽

Structural Domains ◽

Pharmacological Agents ◽

Functional Roles ◽

Cellular Processes ◽

Protein Interactome ◽

Interaction Partners ◽

Recent Developments ◽

Bromodomain Proteins ◽

Chromatin Configuration

Histone acetylation is generally associated with an open chromatin configuration that facilitates many cellular processes including gene transcription, DNA repair, and DNA replication. Aberrant levels of histone lysine acetylation are associated with the development of cancer. Bromodomains represent a family of structurally well-characterized effector domains that recognize acetylated lysines in chromatin. As part of their fundamental reader activity, bromodomain-containing proteins play versatile roles in epigenetic regulation, and additional functional modules are often present in the same protein, or through the assembly of larger enzymatic complexes. Dysregulated gene expression, chromosomal translocations, and/or mutations in bromodomain-containing proteins have been correlated with poor patient outcomes in cancer. Thus, bromodomains have emerged as a highly tractable class of epigenetic targets due to their well-defined structural domains, and the increasing ease of designing or screening for molecules that modulate the reading process. Recent developments in pharmacological agents that target specific bromodomains has helped to understand the diverse mechanisms that bromodomains play with their interaction partners in a variety of chromatin processes, and provide the promise of applying bromodomain inhibitors into the clinical field of cancer treatment. In this review, we explore the expression and protein interactome profiles of bromodomain-containing proteins and discuss them in terms of functional groups. Furthermore, we highlight our current understanding of the roles of bromodomain-containing proteins in cancer, as well as emerging strategies to specifically target bromodomains, including combination therapies using bromodomain inhibitors alongside traditional therapeutic approaches designed to re-program tumorigenesis and metastasis.

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ACTN4 Mediates SEPT14 Mutation-Induced Sperm Head Defects

Biomedicines ◽

10.3390/biomedicines8110518 ◽

2020 ◽

Vol 8 (11) ◽

pp. 518

Author(s):

Yu-Hua Lin ◽

Chia-Yen Huang ◽

Chih-Chun Ke ◽

Ya-Yun Wang ◽

Tsung-Hsuan Lai ◽

...

Keyword(s):

Mass Spectrometry ◽

Cell Model ◽

Membrane Dynamics ◽

Sperm Head ◽

Cellular Processes ◽

Germ Cell Line ◽

Head Formation ◽

Fourth Component ◽

Related Proteins ◽

Cellular Components

Septins (SEPTs) are highly conserved GTP-binding proteins and the fourth component of the cytoskeleton. Polymerized SEPTs participate in the modulation of various cellular processes, such as cytokinesis, cell polarity, and membrane dynamics, through their interactions with microtubules, actin, and other cellular components. The main objective of this study was to dissect the molecular pathological mechanism of SEPT14 mutation-induced sperm head defects. To identify SEPT14 interactors, co-immunoprecipitation (co-IP) and nano-liquid chromatography-mass spectrometry/mass spectrometry were applied. Immunostaining showed that SEPT14 was significantly localized to the manchette structure. The SEPT14 interactors were identified and classified as (1) SEPT-, (2) microtubule-, (3) actin-, and (4) sperm structure-related proteins. One interactor, ACTN4, an actin-holding protein, was selected for further study. Co-IP experiments showed that SEPT14 interacts with ACTN4 in a male germ cell line. SEPT14 also co-localized with ACTN4 in the perinuclear and manchette regions of the sperm head in early elongating spermatids. In the cell model, mutated SEPT14 disturbed the localization pattern of ACTN4. In a clinical aspect, sperm with mutant SEPT14, SEPT14A123T (p.Ala123Thr), and SEPT14I333T (p.Ile333Thr), have mislocalized and fragmented ACTN4 signals. Sperm head defects in donors with SEPT14 mutations are caused by disruption of the functions of ACTN4 and actin during sperm head formation.

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The organisation and functions of local Ca2+ signals

Journal of Cell Science ◽

10.1242/jcs.114.12.2213 ◽

2001 ◽

Vol 114 (12) ◽

pp. 2213-2222 ◽

Cited By ~ 5

Author(s):

Martin D. Bootman ◽

Peter Lipp ◽

Michael J. Berridge

Keyword(s):

Cell Proliferation ◽

Gene Transcription ◽

Cell Biology ◽

Building Blocks ◽

Cell Types ◽

Diverse Range ◽

Cellular Processes ◽

Different Cell Types ◽

Intracellular Messenger ◽

Sensory Mechanisms

Calcium (Ca2+) is a ubiquitous intracellular messenger, controlling a diverse range of cellular processes, such as gene transcription, muscle contraction and cell proliferation. The ability of a simple ion such as Ca2+ to play a pivotal role in cell biology results from the facility that cells have to shape Ca2+ signals in space, time and amplitude. To generate and interpret the variety of observed Ca2+ signals, different cell types employ components selected from a Ca2+ signalling ‘toolkit’, which comprises an array of homeostatic and sensory mechanisms. By mixing and matching components from the toolkit, cells can obtain Ca2+ signals that suit their physiology. Recent studies have demonstrated the importance of local Ca2+ signals in defining the specificity of the interaction of Ca2+ with its targets. Furthermore, local Ca2+ signals are the triggers and building blocks for larger global signals that propagate throughout cells.

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Learning from heterogeneous data sources: an application in spatial proteomics

10.1101/022152 ◽

2015 ◽

Cited By ~ 1

Author(s):

Lisa M. Breckels ◽

Sean Holden ◽

David Wojnar ◽

Claire M. Mulvey ◽

Andy Christoforou ◽

...

Keyword(s):

Mass Spectrometry ◽

Support Vector Machine ◽

Transfer Learning ◽

High Throughput ◽

Cell Biology ◽

Heterogeneous Data ◽

Data Sources ◽

Support Vector ◽

Proteomics Data ◽

Heterogeneous Data Sources

AbstractSub-cellular localisation of proteins is an essential post-translational regulatory mechanism that can be assayed using high-throughput mass spectrometry (MS). These MS-based spatial proteomics experiments enable us to pinpoint the sub-cellular distribution of thousands of proteins in a specific system under controlled conditions. Recent advances in high-throughput MS methods have yielded a plethora of experimental spatial proteomics data for the cell biology community. Yet, there are many third-party data sources, such as immunofluorescence microscopy or protein annotations and sequences, which represent a rich and vast source of complementary information. We present a unique transfer learning classification framework that utilises a nearest-neighbour or support vector machine system, to integrate heterogeneous data sources to considerably improve on the quantity and quality of sub-cellular protein assignment. We demonstrate the utility of our algorithms through evaluation of five experimental datasets, from four different species in conjunction with four different auxiliary data sources to classify proteins to tens of sub-cellular compartments with high generalisation accuracy. We further apply the method to an experiment on pluripotent mouse embryonic stem cells to classify a set of previously unknown proteins, and validate our findings against a recent high resolution map of the mouse stem cell proteome. The methodology is distributed as part of the open-source Bioconductor pRoloc suite for spatial proteomics data analysis.AbbreviationsLOPITLocalisation of Organelle Proteins by Isotope TaggingPCPProtein Correlation ProfilingMLMachine learningTLTransfer learningSVMSupport vector machinePCAPrincipal component analysisGOGene OntologyCCCellular compartmentiTRAQIsobaric tags for relative and absolute quantitationTMTTandem mass tagsMSMass spectrometry

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Extensive non-canonical phosphorylation in human cells revealed using strong-anion exchange-mediated phosphoproteomics

10.1101/202820 ◽

2017 ◽

Cited By ~ 7

Author(s):

Gemma Hardman ◽

Simon Perkins ◽

Zheng Ruan ◽

Natarajan Kannan ◽

Philip Brownridge ◽

...

Keyword(s):

Mass Spectrometry ◽

Protein Phosphorylation ◽

Anion Exchange ◽

Human Cell ◽

Cell Biology ◽

Human Cells ◽

Phosphopeptide Enrichment ◽

Cell Extracts ◽

Strong Anion Exchange ◽

Acid Labile

Protein phosphorylation is a ubiquitous post-translational modification (PTM) that regulates all aspects of life. To date, investigation of human cell signalling has focussed on canonical phosphorylation of serine (Ser), threonine (Thr) and tyrosine (Tyr) residues. However, mounting evidence suggests that phosphorylation of histidine also plays a central role in regulating cell biology. Phosphoproteomics workflows rely on acidic conditions for phosphopeptide enrichment, which are incompatible with the analysis of acid-labile phosphorylation such as histidine. Consequently, the extent of non-canonical phosphorylation is likely to be under-estimated. We report an Unbiased Phosphopeptide enrichment strategy based on Strong Anion Exchange (SAX) chromatography (UPAX), which permits enrichment of acid-labile phosphopeptides for characterisation by mass spectrometry. Using this approach, we identify extensive and positional phosphorylation patterns on histidine, arginine, lysine, aspartate and glutamate in human cell extracts, including 310 phosphohistidine and >1000 phospholysine sites of protein modification. Remarkably, the extent of phosphorylation on individual non-canonical residues vastly exceeds that of basal phosphotyrosine. Our study reveals the previously unappreciated diversity of protein phosphorylation in human cells, and opens up avenues for exploring roles of acid-labile phosphorylation in any proteome using mass spectrometry.

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Characterization of Plasmodium falciparum NEDD8 and identification of cullins as its substrates

10.1101/2020.07.21.213488 ◽

2020 ◽

Author(s):

Manish Bhattacharjee ◽

Navin Adhikari ◽

Renu Sudhakar ◽

Zeba Rizvi ◽

Divya Das ◽

...

Keyword(s):

Mass Spectrometry ◽

Plasmodium Falciparum ◽

Western Blot ◽

Wild Type ◽

Malaria Parasites ◽

Post Translational Modifications ◽

Functional Conservation ◽

Cellular Processes ◽

Physiological Substrates

ABSTRACTA variety of post-translational modifications of Plasmodium falciparum proteins, including phosphorylation and ubiquitination, are shown to have key regulatory roles. The neural precursor cell expressed developmentally downregulated protein 8 (NEDD8) is a ubiquitin-like modifier of cullin-RING E3 ubiquitin ligases, which regulate diverse cellular processes, including the cell-cycle. Although neddylation pathway is conserved in eukaryotes, it is yet to be characterized in Plasmodium and related apicomplexan parasites. Towards studying the neddylation pathway in malaria parasites, we characterized P. falciparum NEDD8 (PfNEDD8) and identified cullins as its physiological substrates. PfNEDD8 is a 76 amino acid residue protein without the C-terminal tail, indicating that it can be readily conjugated. The wild type and mutant (Gly75Gly76 mutated to Ala75Ala76) PfNEDD8 were expressed in P. falciparum. Western blot of wild type PfNEDD8-expressing parasites indicated multiple high molecular weight conjugates, which were absent in the parasites expressing the mutant, indicating conjugation of NEDD8 to proteins through Gly76. Immunoprecipitation followed by mass spectrometry of wild type PfNEDD8-expressing parasites identified several proteins, including two putative cullins. Furthermore, we expressed PfNEDD8 in mutant S. cerevisiae strains that lacked endogenous NEDD8 (Δrub1) or NEDD8 conjugating E2 enzyme (ΔUbc12). The western blot of complemented strains and mass spectrometry of PfNEDD8 immunoprecipitate showed conjugation of PfNEDD8 to S. cerevisiae cullin cdc53, demonstrating functional conservation and cullins as the physiological substrates of PfNEDD8. The characterization of PfNEDD8 and identification of cullins as its substrates make ground for investigation of specific roles and drug target potential of neddylation pathway in malaria parasites.

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