Subcellular Localization in Bacteria: from Envz/Ompr to Transertion
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Uniloc: a Universal Protein Localization Site Predictor For
bioRxiv preprint doi: https://doi.org/10.1101/252916; this version posted January 25, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. UniLoc: A universal protein localization site predictor for eukaryotes and prokaryotes Hsin-Nan Lin, Ching-Tai Chen, Ting-Yi Sung* and Wen-Lian Hsu* Institute of Information Science, Academia Sinica, Taipei, Taiwan * To whom correspondence should be addressed. Tel: +886-2-2788-3799; Fax: +886-2-2782-4814; Email: [email protected]. Correspondence may also be addressed to [email protected]. ABSTRACT There is a growing gap between protein subcellular localization (PSL) data and protein sequence data, raising the need for computation methods to rapidly determine subcellular localizations for uncharacterized proteins. Currently, the most efficient computation method involves finding sequence-similar proteins (hereafter referred to as similar proteins) in the annotated database and transferring their annotations to the target protein. When a sequence-similarity search fails to find similar proteins, many PSL predictors adopt machine learning methods for the prediction of localization sites. We proposed a universal protein localization site predictor - UniLoc - to take advantage of implicit similarity among proteins through sequence analysis alone. The notion of related protein words is introduced to explore the localization site assignment of uncharacterized proteins. UniLoc is found to identify useful template proteins and produce reliable predictions when similar proteins were not available. -
Evidence That Subcellular Localization of a Bacterial Membrane Protein Is Achieved by Diffusion and Capture
Evidence that subcellular localization of a bacterial membrane protein is achieved by diffusion and capture David Z. Rudner, Qi Pan, and Richard M. Losick* Department of Molecular and Cellular Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138 Contributed by Richard M. Losick, April 16, 2002 Bacteria lack an endoplasmic reticulum, a Golgi apparatus, and uted uniformly throughout the cell. In the third model, which we transport vesicles and yet are capable of sorting and delivering call diffusion and capture, the protein is inserted randomly into integral membrane proteins to particular sites within the cell with all membranes and becomes localized by diffusion to, and high precision. What is the pathway by which membrane proteins capture at, the site where it will ultimately reside. reach their proper subcellular destination in bacteria? We have An attractive system in which to address the question of how addressed this question by using green fluorescent protein (GFP) membrane proteins localize is the process of sporulation in B. fused to a polytopic membrane protein (SpoIVFB) that is involved subtilis. Sporulation takes place in two principal morphological in the process of sporulation in the bacterium Bacillus subtilis. stages (7). In the first stage, the sporulating cell (or sporangium) SpoIVFB-GFP localizes to a region of the sporulating cell known as divides asymmetrically through the formation of a polar septum, the outer forespore membrane, which is distinct from the cyto- which creates a small cell known as the forespore and a larger cell plasmic membrane. Experiments are presented that rule out a called the mother cell. Initially, the forespore and mother cell lie mechanism in which SpoIVFB-GFP localizes to all membranes but is side-by-side, but in the second stage of development the fore- selectively eliminated from the cytoplasmic membrane by proteo- spore is engulfed by the mother cell. -
Bird Eye View of Protein Subcellular Localization Prediction
life Review Bird Eye View of Protein Subcellular Localization Prediction Ravindra Kumar 1,* and Sandeep Kumar Dhanda 2,* 1 Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, NIH, 9609 Medical Center Drive, Rockville, MD 20850, USA 2 Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA * Correspondence: [email protected] (R.K.); [email protected] (S.K.D.) Received: 24 November 2020; Accepted: 11 December 2020; Published: 14 December 2020 Abstract: Proteins are made up of long chain of amino acids that perform a variety of functions in different organisms. The activity of the proteins is determined by the nucleotide sequence of their genes and by its 3D structure. In addition, it is essential for proteins to be destined to their specific locations or compartments to perform their structure and functions. The challenge of computational prediction of subcellular localization of proteins is addressed in various in silico methods. In this review, we reviewed the progress in this field and offered a bird eye view consisting of a comprehensive listing of tools, types of input features explored, machine learning approaches employed, and evaluation matrices applied. We hope the review will be useful for the researchers working in the field of protein localization predictions. Keywords: protein localization; signal peptide-based method; sequence compositional information-based method; machine learning based method; integrated method 1. Introduction Proteins are localized into different cellular compartments and sub-compartments inside the cell. Each subcellular compartment has a distinct well-defined function in the cell and has a characteristic physicochemical environment, which drives proper functioning of the proteins. -
Subcellular Localization of a Bacterial Regulatory RNA
Subcellular localization of a bacterial regulatory RNA Jay H. Russell and Kenneth C. Keiler1 The Pennsylvania State University, Department of Biochemistry and Molecular Biology, 401 Althouse Lab, University Park, PA 16802 Edited by Robert T. Sauer, Massachusetts Institute of Technology, Cambridge, MA, and approved July 13, 2009 (received for review May 4, 2009) Eukaryotes and bacteria regulate the activity of some proteins by synchronized cultures of cells in G1 phase, called swarmer cells. localizing them to discrete subcellular structures, and eukaryotes Swarmer cells execute a developmental program that coordi- localize some RNAs for the same purpose. To explore whether nates initiation of DNA replication with morphological differ- bacteria also spatially regulate RNAs, the localization of tmRNA entiation into stalked cells. During differentiation, the polar was determined using fluorescence in situ hybridization. tmRNA is flagellum is ejected and a stalk grows at the same site. Stalked a small regulatory RNA that is ubiquitous in bacteria and that cells complete S phase and divide, producing a stalked cell and interacts with translating ribosomes in a reaction known as trans- a new swarmer cell. trans-Translation is required for correct translation. In Caulobacter crescentus, tmRNA was localized in a timing of events during the developmental program. Cells lack- cell-cycle–dependent manner. In G1-phase cells, tmRNA was found ing ssrA (the gene encoding tmRNA) or smpB do not initiate in regularly spaced foci indicative of a helix-like structure. After DNA replication at the correct time, and all subsequent cell- initiation of DNA replication, most of the tmRNA was degraded, cycle–regulated events are delayed. -
Term Generalization and Synonym Resolution for Biological Abstracts: Using the Gene Ontology for Subcellular Localization Prediction
Term Generalization and Synonym Resolution for Biological Abstracts: Using the Gene Ontology for Subcellular Localization Prediction Alona Fyshe Duane Szafron Department of Computing Science Department of Computing Science University of Alberta University of Alberta Edmonton, Alberta T6G 2E8 Edmonton, Alberta T6G 2E8 [email protected] [email protected] Abstract domain. Our prototype method predicts the subcel- lular localization of proteins (the part of the biolog- The field of molecular biology is growing ical cell where a protein performs its function) by at an astounding rate and research findings performing text classification on related journal ab- are being deposited into public databases, stracts. such as Swiss-Prot. Many of the over In the last two decades, there has been explosive 200,000 protein entries in Swiss-Prot 49.1 growth in molecular biology research. Molecular bi- lack annotations such as subcellular lo- ologists organize their findings into a common set calization or function, but the vast major- of databases. One such database is Swiss-Prot, in ity have references to journal abstracts de- which each entry corresponds to a protein. As of scribing related research. These abstracts version 49.1 (February 21, 2006) Swiss-Prot con- represent a huge amount of information tains more than 200,000 proteins, 190,000 of which that could be used to generate annotations link to biological journal abstracts. Unfortunately, a for proteins automatically. Training clas- much smaller percentage of protein entries are anno- sifiers to perform text categorization on tated with other types of information. For example, abstracts is one way to accomplish this only about half the entries have subcellular localiza- task. -
Biological Circuits with Small RNA Switches
Downloaded from genesdev.cshlp.org on September 24, 2021 - Published by Cold Spring Harbor Laboratory Press REVIEW Stealth regulation: biological circuits with small RNA switches Susan Gottesman Laboratory of Molecular Biology, National Cancer Institute, Bethesda, Maryland 20892, USA So you thinkyou finally understand the regulation of temporal RNAs (stRNAs) or microRNAs, and that these your favorite gene? The transcriptional regulators have RNAs are processed by some of the same protein cofac- been identified; the signaling cascades that regulate syn- tors as is RNAi, have put regulatory RNAs in the spot- thesis and activity of the regulators have been found. light in eukaryotes as well. Recent searches have con- Possibly you have found that the regulator is itself un- firmed that flies, worms, plants, and humans all harbor stable, and that instability is necessary for proper regu- significant numbers of small RNAs likely to play regu- lation. Time to lookfor a new project, or retire and rest latory roles. on your laurels? Not so fast—there’s more. It is rapidly Along with the rapid expansion in RNAs doing inter- becoming apparent that another whole level of regula- esting things, has come a proliferation of nomenclature. tion lurks, unsuspected, in both prokaryotic and eukary- Noncoding RNAs (ncRNA) has been used recently, as otic cells, hidden from our notice in part by the tran- the most general term (Storz 2002). Among the noncod- scription-based approaches that we usually use to study ing RNAs, the subclass of relatively small RNAs that gene regulation, and in part because these regulators are frequently act as regulators have been called stRNAs very small targets for mutagenesis and are not easily (small temporal RNAs, eukaryotes) and sRNAs (small found from genome sequences alone. -
Fur Is the Master Regulator of the Extraintestinal Pathogenic
Downloaded from RESEARCH ARTICLE crossmark Fur Is the Master Regulator of the Extraintestinal Pathogenic mbio.asm.org Escherichia coli Response to Serum on August 3, 2015 - Published by Sagi Huja,a Yaara Oren,a Dvora Biran,a Susann Meyer,b Ulrich Dobrindt,c Joerg Bernhard,b Doerte Becher,b Michael Hecker,b Rotem Sorek,d Eliora Z. Rona,e Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israela; Institute for Microbiology, Ernst-Moritz-Arndt-Universität, Greifswald, Germanyb; Institute of Hygiene, Westfälische Wilhelms-Universität, Münster, Germanyc; Department of Molecular Genetics Weizmann Institute of Science, Rehovot, Israeld; MIGAL, Galilee Research Center, Kiriat Shmona, Israele ABSTRACT Drug-resistant extraintestinal pathogenic Escherichia coli (ExPEC) strains are the major cause of colisepticemia (coli- bacillosis), a condition that has become an increasing public health problem in recent years. ExPEC strains are characterized by high resistance to serum, which is otherwise highly toxic to most bacteria. To understand how these bacteria survive and grow in serum, we performed system-wide analyses of their response to serum, making a clear distinction between the responses to nu- tritional immunity and innate immunity. Thus, mild heat inactivation of serum destroys the immune complement and abolishes mbio.asm.org the bactericidal effect of serum (inactive serum), making it possible to examine nutritional immunity. We used a combination of deep RNA sequencing and proteomics in order to characterize ExPEC genes whose expression is affected by the nutritional stress of serum and by the immune complement. The major change in gene expression induced by serum—active and inactive—in- volved metabolic genes. -
Journal of Microbiological Methods a Proteome-Wide Screen to Identify Transcription Factors Interacting with the Vibrio Cholerae
Journal of Microbiological Methods 165 (2019) 105702 Contents lists available at ScienceDirect Journal of Microbiological Methods journal homepage: www.elsevier.com/locate/jmicmeth Note A proteome-wide screen to identify transcription factors interacting with the Vibrio cholerae rpoS promoter T ⁎ ⁎ Julio C. Ayala1, Jorge A. Benitez , Anisia J. Silva Morehouse School of Medicine, Department of Microbiology, Biochemistry and Immunology, 720 Westview Dr., SW, Atlanta, GA 30310, USA ABSTRACT We describe a proteomic approach to identify transcription factors binding to a target promoter. The method's usefulness was tested by identifying proteins binding to the Vibrio cholerae rpoS promoter in response to cell density. Proteins identified in this screen included the nucleoid-associated protein Fis and the quorum sensing regulator HapR. Isolation of regulatory mutants has played a major role in increasing with agitation at 37 °C to stationary phase. Culture media were sup- our understanding of the regulation of gene expression (Shuman and plemented with ampicillin (Amp, 100 μg/mL), kanamycin (Km, 25 μg/ Silhavy, 2003). There are cases, however, in which the above approach mL), polymyxin B (PolB, 100 units/mL) or L-arabinose (0.2%) as re- can encounter significant obstacles. For instance, the methods used to quired. Chromosomal deletions of fis and/or hapR were created in strain genetically manipulate model organisms are not always equally effec- C7258ΔlacZ by allelic exchange as described previously (Wang et al., tive in less studied microorganisms; some regulatory mutations can be 2011; Wang et al., 2012; Wang et al., 2014). Briefly, genomic DNA highly pleiotropic, often be deleterious, unstable and difficult to select. -
Genome-Wide Transcriptional Response to Varying Rpos Levels
RESEARCH ARTICLE crossm Genome-Wide Transcriptional Response Downloaded from to Varying RpoS Levels in Escherichia coli K-12 Garrett T. Wong,a* Richard P. Bonocora,b Alicia N. Schep,a* Suzannah M. Beeler,a* Anna J. Lee Fong,a* Lauren M. Shull,a* Lakshmi E. Batachari,a Moira Dillon,a Ciaran Evans,c* Carla J. Becker,a Eliot C. Bush,a Johanna Hardin,c http://jb.asm.org/ Joseph T. Wade,b,d Daniel M. Stoebela Department of Biology, Harvey Mudd College, Claremont, California, USAa; Wadsworth Center, New York State Department of Health, Albany, New York, USAb; Department of Mathematics, Pomona College, Claremont, California, USAc; Department of Biomedical Sciences, School of Public Health, University at Albany, SUNY, Albany, New York, USAd ABSTRACT The alternative sigma factor RpoS is a central regulator of many stress on April 17, 2017 by CALIFORNIA INSTITUTE OF TECHNOLOGY responses in Escherichia coli. The level of functional RpoS differs depending on the Received 21 October 2016 Accepted 12 stress. The effect of these differing concentrations of RpoS on global transcriptional January 2017 Accepted manuscript posted online 23 responses remains unclear. We investigated the effect of RpoS concentration on the January 2017 transcriptome during stationary phase in rich media. We found that 23% of genes in Citation Wong GT, Bonocora RP, Schep AN, the E. coli genome are regulated by RpoS, and we identified many RpoS-transcribed Beeler SM, Lee Fong AJ, Shull LM, Batachari LE, genes and promoters. We observed three distinct classes of response to RpoS by Dillon M, Evans C, Becker CJ, Bush EC, Hardin J, Wade JT, Stoebel DM. -
Regulatory Interplay Between Small Rnas and Transcription Termination Factor Rho Lionello Bossi, Nara Figueroa-Bossi, Philippe Bouloc, Marc Boudvillain
Regulatory interplay between small RNAs and transcription termination factor Rho Lionello Bossi, Nara Figueroa-Bossi, Philippe Bouloc, Marc Boudvillain To cite this version: Lionello Bossi, Nara Figueroa-Bossi, Philippe Bouloc, Marc Boudvillain. Regulatory interplay be- tween small RNAs and transcription termination factor Rho. Biochimica et Biophysica Acta - Gene Regulatory Mechanisms , Elsevier, 2020, pp.194546. 10.1016/j.bbagrm.2020.194546. hal-02533337 HAL Id: hal-02533337 https://hal.archives-ouvertes.fr/hal-02533337 Submitted on 6 Nov 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Regulatory interplay between small RNAs and transcription termination factor Rho Lionello Bossia*, Nara Figueroa-Bossia, Philippe Bouloca and Marc Boudvillainb a Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France b Centre de Biophysique Moléculaire, CNRS UPR4301, rue Charles Sadron, 45071 Orléans cedex 2, France * Corresponding author: [email protected] Highlights Repression -
Osmosensing by the Bacterial Phoq/Phop Two-Component System
Osmosensing by the bacterial PhoQ/PhoP two-component system Jing Yuana,b,1, Fan Jina,b, Timo Glattera, and Victor Sourjika,b,1 aMax Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany; and bLOEWE Center for Synthetic Microbiology (SYNMIKRO), 35043 Marburg, Germany Edited by Susan Gottesman, National Institutes of Health, Bethesda, MD, and approved November 6, 2017 (received for review October 5, 2017) The PhoQ/PhoP two-component system plays an essential role in domain and the cytoplasmic domains (10, 11), with the latter the response of enterobacteria to the environment of their mam- detecting the cytoplasmic pH change. The PhoQ TM domain is a malian hosts. It is known to sense several stimuli that are poten- dimer of two TM helices that form a four-helix bundle (12). tially associated with the host, including extracellular magnesium Upon activation of the sensory domain, the periplasmic ends of limitation, low pH, and the presence of cationic antimicrobial the two TM1 helices move closer to each other and push the two peptides. Here, we show that the PhoQ/PhoP two-component TM2 helices farther apart, accompanied by a TM2 rotation, systems of Escherichia coli and Salmonella can also perceive an which requires the solvation of a semichannel in the four-helix osmotic upshift, another key stimulus to which bacteria become bundle (12). Asn202, located near the center of the TM2 helix exposed within the host. In contrast to most previously estab- and proximal to this semichannel, affects the solvation of the lished stimuli of PhoQ, the detection of osmotic upshift does not cavity, and mutations of Asn202 to a nonpolar residue lock PhoQ require its periplasmic sensor domain. -
Vimentin) ScaOld
Oncogene (1998) 16, 3423 ± 3434 1998 Stockton Press All rights reserved 0950 ± 9232/98 $12.00 http://www.stockton-press.co.uk/onc Cytoplasmic retention of mutant tsp53 is dependent on an intermediate ®lament protein (Vimentin) scaold Oliver Klotzsche1,DoÈrte Etzrodt2, Heinz Hohenberg1, Wolfgang Bohn1 and Wolfgang Deppert1 1Heinrich-Pette-Institut fuÈr Experimentelle Virologie und Immunologie an der UniversitaÈt Hamburg, Martinistr. 52, D-20251 Hamburg, Germany The temperature-sensitive mutant tsp53val135 accumulates these mutations do not simply inactivate the tumor in the cytoplasm of cells kept at the non-permissive suppressor functions of wild-type (wt) p53, but provide temperature (398C), but is rapidly transported into the a `gain of function' for the mutant (mt) p53 (Deppert, cell nucleus at the permissive temperature (308C). tsp53 1996; Dittmer et al., 1993). This hypothesis is thus may serve as a model for analysing cellular supported by a variety of biological and biochemical parameters in¯uencing the subcellular location of p53. observations, which strongly suggest that mt p53 exerts Here we provide evidence that retention of tsp53 in the properties of a dominant oncogene. cytoplasm at the non-permissive temperature is due to The multitude of functions ascribed to either wt or cytoskeletal anchorage of the p53 protein. Two sublines mt p53 requires that the functional properties of these of C6 rat glioma cells diering in their expression of the proteins are tightly and coordinatedly regulated. In intermediate ®lament protein vimentin (vimentin expres- addition to various posttranslational modi®cations and sing or vimentin negative cells) were stably transfected interactions with viral and cellular proteins (Deppert, with a vector encoding tsp53.