Coupling chemosensory array formation and localization

Chemotaxis proteins organize into large, highly ordered, chemotactic signaling arrays, which in Vibrio species are found at the cell pole. Proper localization of signaling arrays is mediated by ParP, which tethers arrays to a cell pole anchor, ParC. Here we show that ParP’s C-terminus integrates into the core-unit of signaling arrays through interactions with MCP-proteins and CheA. Its intercalation within core-units stimulates array formation, whereas its N-terminal interaction domain enables polar recruitment of arrays and facilitates its own polar localization. Linkage of these domains within ParP couples array formation and localization and results in controlled array positioning at the cell pole. Notably, ParP’s integration into arrays modifies its own and ParC’s subcellular localization dynamics, promoting their polar retention. ParP serves as a critical nexus that regulates the localization dynamics of its network constituents and drives the localized assembly and stability of the chemotactic machinery, resulting in proper cell pole development.

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Faculty Opinions recommendation of A family of ParA-like ATPases promotes cell pole maturation by facilitating polar localization of chemotaxis proteins.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.12262956.13437054 ◽

2011 ◽

Author(s):

George Ordal

Keyword(s):

Polar Localization ◽

Cell Pole ◽

Chemotaxis Proteins

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The Hypoxia-Associated Localization of Chemotaxis Protein CheZ in Azorhizorbium caulinodans

Frontiers in Microbiology ◽

10.3389/fmicb.2021.731419 ◽

2021 ◽

Vol 12 ◽

Author(s):

Xiaolin Liu ◽

Yanan Liu ◽

Yixuan Wang ◽

Dandan Wang ◽

Kevin Scot Johnson ◽

...

Keyword(s):

Cellular Localization ◽

Spatial Organization ◽

Energy Status ◽

Cellular Functions ◽

Factors Affecting ◽

Polar Localization ◽

C Terminus ◽

Chemotaxis Proteins ◽

Chemotaxis System ◽

External Stimuli

Spatial organization of chemotactic proteins is important for cooperative response to external stimuli. However, factors affecting the localization dynamics of chemotaxis proteins are less studied. According to some reports, had found that the polar localization of chemotaxis system I is induced by hypoxia and starvation in Vibrio cholerae. However, in V. cholerae, the chemotaxis system I is not involved in flagellum-mediated chemotaxis, and it may play other alternative cellular functions. In this study, we found that the polar localization of CheZ, a phosphatase regulating chemotactic movement in Azorhizobium caulinodans ORS571, can also be affected by hypoxia and cellular energy-status. The conserved phosphatase active site D165 and the C-terminus of CheZ are essential for the energy-related localization, indicating a cross link between hypoxia-related localization changes and phosphatase activity of CheZ. Furthermore, three of five Aer-like chemoreceptors containing PAS domains participate in the cellular localization of CheZ. In contrast to carbon starvation, free-living nitrogen fixation can alleviate the role of nitrogen limitation and hypoxia on polar localization of CheZ. These results showed that the localization changes induced by hypoxia might be a strategy for bacteria to adapt to complex environment.

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Polar Localization of CheA2 in Rhodobacter sphaeroides Requires Specific Che Homologs

Journal of Bacteriology ◽

10.1128/jb.185.16.4667-4671.2003 ◽

2003 ◽

Vol 185 (16) ◽

pp. 4667-4671 ◽

Cited By ~ 10

Author(s):

Angela C. Martin ◽

Usha Nair ◽

Judith P. Armitage ◽

Janine R. Maddock

Keyword(s):

Subcellular Localization ◽

Rhodobacter Sphaeroides ◽

Subcellular Location ◽

Growth Conditions ◽

Aerobic Conditions ◽

E Coli ◽

Polar Localization ◽

Chemotaxis Proteins ◽

Motile Bacterium ◽

Photoheterotrophic Growth

ABSTRACT Rhodobacter sphaeroides is a motile bacterium that has multiple chemotaxis genes organized predominantly in three major operons (cheOp1, cheOp2, and cheOp3). The chemoreceptor proteins are clustered at two distinct locations, the cell poles and in one or more cytoplasmic clusters. One intriguing possibility is that the physically distinct chemoreceptor clusters are each composed of a defined subset of specific chemotaxis proteins, including the chemoreceptors themselves plus specific CheW and CheA proteins. Here we report the subcellular localization of one such protein, CheA2, under aerobic and photoheterotrophic growth conditions. CheA2 is predominantly clustered and localized at the cell poles under both growth conditions. Furthermore, its localization is dependent upon one or more genes in cheOp2 but not those of cheOp1 or cheOp3. In E. coli, the polar localization of CheA depends upon CheW. The R. sphaeroides cheOp2 contains two cheW genes. Interestingly, CheW2 is required under both aerobic and photoheterotrophic conditions, whereas CheW3 is not required under aerobic conditions but appears to play a modest role under photoheterotrophic conditions. This suggests that R. sphaeroides contains at least two distinct chemotaxis complexes, possibly composed of proteins dedicated for each subcellular location. Furthermore, the composition of these spatially distinct complexes may change under different growth conditions.

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Interdependent Polar Localization of FlhF and FlhG and Their Importance for Flagellum Formation of Vibrio parahaemolyticus

Frontiers in Microbiology ◽

10.3389/fmicb.2021.655239 ◽

2021 ◽

Vol 12 ◽

Author(s):

Erick Eligio Arroyo-Pérez ◽

Simon Ringgaard

Keyword(s):

Cell Cycle ◽

Vibrio Parahaemolyticus ◽

Intracellular Localization ◽

Dependent Manner ◽

Swimming Ability ◽

Polar Localization ◽

Cell Pole ◽

A Cell ◽

Cycle Dependent ◽

Spatiotemporal Localization

Failure of the cell to properly regulate the number and intracellular positioning of their flagella, has detrimental effects on the cells’ swimming ability. The flagellation pattern of numerous bacteria is regulated by the NTPases FlhF and FlhG. In general, FlhG controls the number of flagella produced, whereas FlhF coordinates the position of the flagella. In the human pathogen Vibrio parahaemolyticus, its single flagellum is positioned and formed at the old cell pole. Here, we describe the spatiotemporal localization of FlhF and FlhG in V. parahaemolyticus and their effect on swimming motility. Absence of either FlhF or FlhG caused a significant defect in swimming ability, resulting in absence of flagella in a ΔflhF mutant and an aberrant flagellated phenotype in ΔflhG. Both proteins localized to the cell pole in a cell cycle-dependent manner, but displayed different patterns of localization throughout the cell cycle. FlhF transitioned from a uni- to bi-polar localization, as observed in other polarly flagellated bacteria. Localization of FlhG was strictly dependent on the cell pole-determinant HubP, while polar localization of FlhF was HubP independent. Furthermore, localization of FlhF and FlhG was interdependent and required for each other’s proper intracellular localization and recruitment to the cell pole. In the absence of HubP or FlhF, FlhG forms non-polar foci in the cytoplasm of the cell, suggesting the possibility of a secondary localization site within the cell besides its recruitment to the cell poles.

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A family of ParA-like ATPases promotes cell pole maturation by facilitating polar localization of chemotaxis proteins

Genes & Development ◽

10.1101/gad.2061811 ◽

2011 ◽

Vol 25 (14) ◽

pp. 1544-1555 ◽

Cited By ~ 63

Author(s):

S. Ringgaard ◽

K. Schirner ◽

B. M. Davis ◽

M. K. Waldor

Keyword(s):

Polar Localization ◽

Cell Pole ◽

Chemotaxis Proteins

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lncLocator 2.0: a cell-line-specific subcellular localization predictor for long non-coding RNAs with interpretable deep learning

Bioinformatics ◽

10.1093/bioinformatics/btab127 ◽

2021 ◽

Author(s):

Yang Lin ◽

Xiaoyong Pan ◽

Hong-Bin Shen

Keyword(s):

Subcellular Localization ◽

Cell Line ◽

Cell Lines ◽

Short Term Memory ◽

Computational Method ◽

Language Models ◽

Supplementary Information ◽

Deep Model ◽

A Cell ◽

Non Coding Rnas

Abstract Motivation Long non-coding RNAs (lncRNAs) are generally expressed in a tissue-specific way, and subcellular localizations of lncRNAs depend on the tissues or cell lines that they are expressed. Previous computational methods for predicting subcellular localizations of lncRNAs do not take this characteristic into account, they train a unified machine learning model for pooled lncRNAs from all available cell lines. It is of importance to develop a cell-line-specific computational method to predict lncRNA locations in different cell lines. Results In this study, we present an updated cell-line-specific predictor lncLocator 2.0, which trains an end-to-end deep model per cell line, for predicting lncRNA subcellular localization from sequences.We first construct benchmark datasets of lncRNA subcellular localizations for 15 cell lines. Then we learn word embeddings using natural language models, and these learned embeddings are fed into convolutional neural network, long short-term memory and multilayer perceptron to classify subcellular localizations. lncLocator 2.0 achieves varying effectiveness for different cell lines and demonstrates the necessity of training cell-line-specific models. Furthermore, we adopt Integrated Gradients to explain the proposed model in lncLocator 2.0, and find some potential patterns that determine the subcellular localizations of lncRNAs, suggesting that the subcellular localization of lncRNAs is linked to some specific nucleotides. Availability The lncLocator 2.0 is available at www.csbio.sjtu.edu.cn/bioinf/lncLocator2 and the source code can be found at https://github.com/Yang-J-LIN/lncLocator2. Supplementary information Supplementary data are available at Bioinformatics online.

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The C Terminus of Foamy Retrovirus Gag Contains Determinants for Encapsidation of Pol Protein into Virions

Journal of Virology ◽

10.1128/jvi.00812-08 ◽

2008 ◽

Vol 82 (21) ◽

pp. 10803-10810 ◽

Cited By ~ 26

Author(s):

Eun-Gyung Lee ◽

Maxine L. Linial

Keyword(s):

Site Directed Mutagenesis ◽

Rna Packaging ◽

Interaction Domain ◽

Virus Particles ◽

Charged Amino Acids ◽

C Terminus ◽

Foamy Viruses ◽

Substitution Mutations ◽

Gag Assembly ◽

Positively Charged

ABSTRACT Foamy viruses (FV) differ from orthoretroviruses in many aspects of their replication cycle. A major difference is in the mode of Pol expression, regulation, and encapsidation into virions. Orthoretroviruses synthesize Pol as a Gag-Pol fusion protein so that Pol is encapsidated into virus particles through Gag assembly domains. However, as FV express Pol independently of Gag from a spliced mRNA, packaging occurs through a distinct mechanism. FV genomic RNA contains cis-acting sequences that are required for Pol packaging, suggesting that Pol binds to RNA for its encapsidation. However, it is not known whether Gag is directly involved in Pol packaging. Previously our laboratory showed that sequences flanking the three glycine-arginine-rich (GR) boxes at the C terminus of FV Gag contain domains important for RNA packaging and Pol expression, cleavage, and packaging. We have now shown that both deletion and substitution mutations in the first GR box (GR1) prevented neither the assembly of particles with wild-type density nor packaging of RNA genomes but led to a defect in Pol packaging. Site-directed mutagenesis of GR1 indicated that the clustered positively charged amino acids in GR1 play important roles in Pol packaging. Our results suggest that GR1 contains a Pol interaction domain and that a Gag-Pol complex is formed and binds to RNA for incorporation into virions.

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The Core Binding Factor (CBF) α Interaction Domain and the Smooth Muscle Myosin Heavy Chain (SMMHC) Segment of CBFβ-SMMHC Are Both Required to Slow Cell Proliferation

Journal of Biological Chemistry ◽

10.1074/jbc.273.47.31534 ◽

1998 ◽

Vol 273 (47) ◽

pp. 31534-31540 ◽

Cited By ~ 24

Author(s):

Wangsen Cao ◽

Neeraj Adya ◽

Martin Britos-Bray ◽

P. Paul Liu ◽

Alan D. Friedman

Keyword(s):

Cell Proliferation ◽

Smooth Muscle ◽

Myosin Heavy Chain ◽

Heavy Chain ◽

Smooth Muscle Myosin ◽

Core Binding Factor ◽

Interaction Domain ◽

The Core ◽

Binding Factor ◽

Muscle Myosin

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Stabilization of Polar Localization of a Chemoreceptor via Its Covalent Modifications and Its Communication with a Different Chemoreceptor

Journal of Bacteriology ◽

10.1128/jb.187.22.7647-7654.2005 ◽

2005 ◽

Vol 187 (22) ◽

pp. 7647-7654 ◽

Cited By ~ 29

Author(s):

Daisuke Shiomi ◽

Satomi Banno ◽

Michio Homma ◽

Ikuro Kawagishi

Keyword(s):

Histidine Kinase ◽

Fluorescent Protein ◽

Adaptor Protein ◽

Molecular Assembly ◽

Covalent Modification ◽

Polar Localization ◽

Receptor Localization ◽

A Cell ◽

Covalent Modifications ◽

Green Fluorescent

ABSTRACT In the chemotaxis of Escherichia coli, polar clustering of the chemoreceptors, the histidine kinase CheA, and the adaptor protein CheW is thought to be involved in signal amplification and adaptation. However, the mechanism that leads to the polar localization of the receptor is still largely unknown. In this study, we examined the effect of receptor covalent modification on the polar localization of the aspartate chemoreceptor Tar fused to green fluorescent protein (GFP). Amidation (and presumably methylation) of Tar-GFP enhanced its own polar localization, although the effect was small. The slight but significant effect of amidation on receptor localization was reinforced by the fact that localization of a noncatalytic mutant version of GFP-CheR that targets to the C-terminal pentapeptide sequence of Tar was similarly facilitated by receptor amidation. Polar localization of the demethylated version of Tar-GFP was also enhanced by increasing levels of the serine chemoreceptor Tsr. The effect of covalent modification on receptor localization by itself may be too small to account for chemotactic adaptation, but receptor modification is suggested to contribute to the molecular assembly of the chemoreceptor/histidine kinase array at a cell pole, presumably by stabilizing the receptor dimer-to-dimer interaction.

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