1
|
Wu R, Barnes S, Dahlin H, Khamrui S, Ingle S, Xiang Y, Shi Y, Bechhofer D, Lazarus M. Structural insights into RNA cleavage by a novel family of bacterial RNases. RESEARCH SQUARE 2023:rs.3.rs-3788707. [PMID: 38234822 PMCID: PMC10793500 DOI: 10.21203/rs.3.rs-3788707/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Processing of RNA is a key regulatory mechanism for all living systems. We recently discovered a novel family of endoribonucleases that is conserved across all bacteria. Here, using crystallography, cryo-EM microscopy, biochemical, biophysical, and mass spectrometry techniques, we are able to shed light on a novel RNA cleavage mechanism in bacteria. We show that YicC, the prototypical member of this family, forms a hexameric channel that closes down on a 26-mer RNA substrate, and find that it cleaves across an RNA hairpin to generate several short fragments.
Collapse
Affiliation(s)
- Ruoxi Wu
- Icahn School of Medicine at Mount Sinai
| | | | | | | | | | | | - Yi Shi
- Icahn School of Medicine at Mount Sinai
| | | | | |
Collapse
|
2
|
Carter EW, Peraza OG, Wang N. The protein interactome of the citrus Huanglongbing pathogen Candidatus Liberibacter asiaticus. Nat Commun 2023; 14:7838. [PMID: 38030598 PMCID: PMC10687234 DOI: 10.1038/s41467-023-43648-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 11/15/2023] [Indexed: 12/01/2023] Open
Abstract
The bacterium Candidatus Liberibacter asiaticus (CLas) causes citrus Huanglongbing disease. Our understanding of the pathogenicity and biology of this microorganism remains limited because CLas has not yet been cultivated in artificial media. Its genome is relatively small and encodes approximately 1136 proteins, of which 415 have unknown functions. Here, we use a high-throughput yeast-two-hybrid (Y2H) screen to identify interactions between CLas proteins, thus providing insights into their potential functions. We identify 4245 interactions between 542 proteins, after screening 916 bait and 936 prey proteins. The false positive rate of the Y2H assay is estimated to be 2.9%. Pull-down assays for nine protein-protein interactions (PPIs) likely involved in flagellar function support the robustness of the Y2H results. The average number of PPIs per node in the CLas interactome is 15.6, which is higher than the numbers previously reported for interactomes of free-living bacteria, suggesting that CLas genome reduction has been accompanied by increased protein multi-functionality. We propose potential functions for 171 uncharacterized proteins, based on the PPI results, guilt-by-association analyses, and comparison with data from other bacterial species. We identify 40 hub-node proteins, including quinone oxidoreductase and LysR, which are known to protect other bacteria against oxidative stress and might be important for CLas survival in the phloem. We expect our PPI database to facilitate research on CLas biology and pathogenicity mechanisms.
Collapse
Affiliation(s)
- Erica W Carter
- Citrus Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL, USA
- Department of Plant Pathology, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL, USA
| | - Orlene Guerra Peraza
- Citrus Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL, USA
| | - Nian Wang
- Citrus Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL, USA.
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL, US.
| |
Collapse
|
3
|
Schwartz AV, Sant KE, George UZ. Development of a Dynamic Network Model to Identify Temporal Patterns of Structural Malformations in Zebrafish Embryos Exposed to a Model Toxicant, Tris(4-chlorophenyl)methanol. J Xenobiot 2023; 13:284-297. [PMID: 37367497 DOI: 10.3390/jox13020021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 05/31/2023] [Accepted: 06/14/2023] [Indexed: 06/28/2023] Open
Abstract
Embryogenesis is a well-coordinated process relying on precise cues and environmental signals that direct spatiotemporal embryonic patterning. Quite often, when one error in this process occurs, others tend to co-occur. We posit that investigating the co-occurrence of these abnormalities over time would yield additional information about the mode of toxicity for chemicals. Here, we use the environmental contaminant tris(4-chlorophenyl)methanol (TCPMOH) as a model toxicant to assess the relationship between exposures and co-occurrence of developmental abnormalities in zebrafish embryos. We propose a dynamic network modeling approach to study the co-occurrence of abnormalities, including pericardial edema, yolk sac edema, cranial malformation, spinal deformity, delayed/failed swim bladder inflation, and mortality induced by TCPMOH exposure. TCPMOH-exposed samples revealed increased abnormality co-occurrence when compared to controls. The abnormalities were represented as nodes in the dynamic network model. Abnormalities with high co-occurrence over time were identified using network centrality scores. We found that the temporal patterns of abnormality co-occurrence varied between exposure groups. In particular, the high TCPMOH exposure group experienced abnormality co-occurrence earlier than the low exposure group. The network model also revealed that pericardial and yolk sac edema are the most common critical nodes among all TCPMOH exposure levels, preceding further abnormalities. Overall, this study introduces a dynamic network model as a tool for assessing developmental toxicology, integrating structural and temporal features with a concentration response.
Collapse
Affiliation(s)
- Ashley V Schwartz
- Computational Science Research Center, San Diego State University, San Diego, CA 92182, USA
- Department of Mathematics and Statistics, San Diego State University, San Diego, CA 92182, USA
| | - Karilyn E Sant
- School of Public Health, Division of Environmental Health, San Diego State University, San Diego, CA 92182, USA
| | - Uduak Z George
- Computational Science Research Center, San Diego State University, San Diego, CA 92182, USA
- Department of Mathematics and Statistics, San Diego State University, San Diego, CA 92182, USA
| |
Collapse
|
4
|
O'Reilly FJ, Graziadei A, Forbrig C, Bremenkamp R, Charles K, Lenz S, Elfmann C, Fischer L, Stülke J, Rappsilber J. Protein complexes in cells by AI-assisted structural proteomics. Mol Syst Biol 2023; 19:e11544. [PMID: 36815589 PMCID: PMC10090944 DOI: 10.15252/msb.202311544] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 01/24/2023] [Accepted: 02/07/2023] [Indexed: 02/24/2023] Open
Abstract
Accurately modeling the structures of proteins and their complexes using artificial intelligence is revolutionizing molecular biology. Experimental data enable a candidate-based approach to systematically model novel protein assemblies. Here, we use a combination of in-cell crosslinking mass spectrometry and co-fractionation mass spectrometry (CoFrac-MS) to identify protein-protein interactions in the model Gram-positive bacterium Bacillus subtilis. We show that crosslinking interactions prior to cell lysis reveals protein interactions that are often lost upon cell lysis. We predict the structures of these protein interactions and others in the SubtiWiki database with AlphaFold-Multimer and, after controlling for the false-positive rate of the predictions, we propose novel structural models of 153 dimeric and 14 trimeric protein assemblies. Crosslinking MS data independently validates the AlphaFold predictions and scoring. We report and validate novel interactors of central cellular machineries that include the ribosome, RNA polymerase, and pyruvate dehydrogenase, assigning function to several uncharacterized proteins. Our approach uncovers protein-protein interactions inside intact cells, provides structural insight into their interaction interfaces, and is applicable to genetically intractable organisms, including pathogenic bacteria.
Collapse
Affiliation(s)
- Francis J O'Reilly
- Chair of BioanalyticsTechnische Universität BerlinBerlinGermany
- Present address:
Center for Structural Biology, Center for Cancer ResearchNational Cancer Institute (NCI)FrederickMDUSA
| | | | | | - Rica Bremenkamp
- Department of General Microbiology, Institute of Microbiology and GeneticsAugust‐University GöttingenGöttingenGermany
| | | | - Swantje Lenz
- Chair of BioanalyticsTechnische Universität BerlinBerlinGermany
| | - Christoph Elfmann
- Department of General Microbiology, Institute of Microbiology and GeneticsAugust‐University GöttingenGöttingenGermany
| | - Lutz Fischer
- Chair of BioanalyticsTechnische Universität BerlinBerlinGermany
| | - Jörg Stülke
- Department of General Microbiology, Institute of Microbiology and GeneticsAugust‐University GöttingenGöttingenGermany
| | - Juri Rappsilber
- Chair of BioanalyticsTechnische Universität BerlinBerlinGermany
- Wellcome Centre for Cell BiologyUniversity of EdinburghEdinburghUK
| |
Collapse
|
5
|
Ventroux M, Noirot-Gros MF. Prophage-encoded small protein YqaH counteracts the activities of the replication initiator DnaA in Bacillus subtilis. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 36748575 DOI: 10.1099/mic.0.001268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Bacterial genomes harbour cryptic prophages that are mostly transcriptionally silent with many unannotated genes. Still, cryptic prophages may contribute to their host fitness and phenotypes. In Bacillus subtilis, the yqaF-yqaN operon belongs to the prophage element skin, and is tightly repressed by the Xre-like repressor SknR. This operon contains several small ORFs (smORFs) potentially encoding small-sized proteins. The smORF-encoded peptide YqaH was previously reported to bind to the replication initiator DnaA. Here, using a yeast two-hybrid assay, we found that YqaH binds to the DNA binding domain IV of DnaA and interacts with Spo0A, a master regulator of sporulation. We isolated single amino acid substitutions in YqaH that abolished the interaction with DnaA but not with Spo0A. Then, using a plasmid-based inducible system to overexpress yqaH WT and mutant derivatives, we studied in B. subtilis the phenotypes associated with the specific loss-of-interaction with DnaA (DnaA_LOI). We found that expression of yqaH carrying DnaA_LOI mutations abolished the deleterious effects of yqaH WT expression on chromosome segregation, replication initiation and DnaA-regulated transcription. When YqaH was induced after vegetative growth, DnaA_LOI mutations abolished the drastic effects of YqaH WT on sporulation and biofilm formation. Thus, YqaH inhibits replication, sporulation and biofilm formation mainly by antagonizing DnaA in a manner that is independent of the cell cycle checkpoint Sda.
Collapse
Affiliation(s)
- Magali Ventroux
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | | |
Collapse
|
6
|
Interrelation between Stress Management and Secretion Systems of Ralstonia solanacearum: An In Silico Assessment. Pathogens 2022; 11:pathogens11070730. [PMID: 35889976 PMCID: PMC9325324 DOI: 10.3390/pathogens11070730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 06/18/2022] [Accepted: 06/24/2022] [Indexed: 11/17/2022] Open
Abstract
Ralstonia solanacearum (Rs), the causative agent of devastating wilt disease in several major and minor economic crops, is considered one of the most destructive bacterial plant pathogens. However, the mechanism(s) by which Rs counteracts host-associated environmental stress is still not clearly elucidated. To investigate possible stress management mechanisms, orthologs of stress-responsive genes in the Rs genome were searched using a reference set of known genes. The genome BLAST approach was used to find the distributions of these orthologs within different Rs strains. BLAST results were first confirmed from the KEGG Genome database and then reconfirmed at the protein level from the UniProt database. The distribution pattern of these stress-responsive factors was explored through multivariate analysis and STRING analysis. STRING analysis of stress-responsive genes in connection with different secretion systems of Rs was also performed. Initially, a total of 28 stress-responsive genes of Rs were confirmed in this study. STRING analysis revealed an additional 7 stress-responsive factors of Rs, leading to the discovery of a total of 35 stress-responsive genes. The segregation pattern of these 35 genes across 110 Rs genomes was found to be almost homogeneous. Increasing interactions of Rs stress factors were observed in six distinct clusters, suggesting six different types of stress responses: membrane stress response (MSR), osmotic stress response (OSR), oxidative stress response (OxSR), nitrosative stress response (NxSR), and DNA damage stress response (DdSR). Moreover, a strong network of these stress responses was observed with type 3 secretion system (T3SS), general secretory proteins (GSPs), and different types of pili (T4P, Tad, and Tat). To the best of our knowledge, this is the first report on overall stress response management by Rs and the potential connection with secretion systems.
Collapse
|
7
|
Saaki TNV, Teng Z, Wenzel M, Ventroux M, Carballido-Lόpez R, Noirot-Gros MF, Hamoen LW. SepF supports the recruitment of the DNA translocase SftA to the Z-ring. Mol Microbiol 2022; 117:1263-1274. [PMID: 35411648 PMCID: PMC9320952 DOI: 10.1111/mmi.14906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 04/07/2022] [Accepted: 04/09/2022] [Indexed: 11/28/2022]
Abstract
In many bacteria, cell division begins before the sister chromosomes are fully segregated. Specific DNA translocases ensure that the chromosome is removed from the closing septum, such as the transmembrane protein FtsK in Escherichia coli. Bacillus subtilis contains two FtsK homologues, SpoIIIE and SftA. SftA is active during vegetative growth whereas SpoIIIE is primarily active during sporulation and pumps the chromosome into the spore compartment. FtsK and SpoIIIE contain several transmembrane helices, however SftA is assumed to be a cytoplasmic protein. It is unknown how SftA is recruited to the cell division site. Here we show that SftA is a peripheral membrane protein, containing an N-terminal amphipathic helix that reversibly anchors the protein to the cell membrane. Using a yeast two-hybrid screen we found that SftA interacts with the conserved cell division protein SepF. Based on extensive genetic analyses and previous data we propose that the septal localization of SftA depends on either SepF or the cell division protein FtsA. Since SftA seems to interfere with the activity of SepF, and since inactivation of SepF mitigates the sensitivity of a ∆sftA mutant for ciprofloxacin, we speculate that SftA might delay septum synthesis when chromosomal DNA is in the vicinity.
Collapse
Affiliation(s)
- Terrens N V Saaki
- Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, Amsterdam, The Netherlands
| | - Zihao Teng
- Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, Amsterdam, The Netherlands
| | - Michaela Wenzel
- Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, Amsterdam, The Netherlands.,current address: Division of Chemical Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Magali Ventroux
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay Jouy-en-Josas, France
| | - Rut Carballido-Lόpez
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay Jouy-en-Josas, France
| | | | - Leendert W Hamoen
- Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, Amsterdam, The Netherlands
| |
Collapse
|
8
|
Abstract
Since the large-scale experimental characterization of protein–protein interactions (PPIs) is not possible for all species, several computational PPI prediction methods have been developed that harness existing data from other species. While PPI network prediction has been extensively used in eukaryotes, microbial network inference has lagged behind. However, bacterial interactomes can be built using the same principles and techniques; in fact, several methods are better suited to bacterial genomes. These predicted networks allow systems-level analyses in species that lack experimental interaction data. This review describes the current network inference and analysis techniques and summarizes the use of computationally-predicted microbial interactomes to date.
Collapse
|
9
|
Shi L, Derouiche A, Pandit S, Rahimi S, Kalantari A, Futo M, Ravikumar V, Jers C, Mokkapati VRSS, Vlahoviček K, Mijakovic I. Evolutionary Analysis of the Bacillus subtilis Genome Reveals New Genes Involved in Sporulation. Mol Biol Evol 2021; 37:1667-1678. [PMID: 32061128 PMCID: PMC7426031 DOI: 10.1093/molbev/msaa035] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Bacilli can form dormant, highly resistant, and metabolically inactive spores to cope with extreme environmental challenges. In this study, we examined the evolutionary age of Bacillus subtilis sporulation genes using the approach known as genomic phylostratigraphy. We found that B. subtilis sporulation genes cluster in several groups that emerged at distant evolutionary time-points, suggesting that the sporulation process underwent several stages of expansion. Next, we asked whether such evolutionary stratification of the genome could be used to predict involvement in sporulation of presently uncharacterized genes (y-genes). We individually inactivated a representative sample of uncharacterized genes that arose during the same evolutionary periods as the known sporulation genes and tested the resulting strains for sporulation phenotypes. Sporulation was significantly affected in 16 out of 37 (43%) tested strains. In addition to expanding the knowledge base on B. subtilis sporulation, our findings suggest that evolutionary age could be used to help with genome mining.
Collapse
Affiliation(s)
- Lei Shi
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Abderahmane Derouiche
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Santosh Pandit
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Shadi Rahimi
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Aida Kalantari
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Momir Futo
- Laboratory of Evolutionary Genetics, Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
| | - Vaishnavi Ravikumar
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Carsten Jers
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Venkata R S S Mokkapati
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Kristian Vlahoviček
- Bioinformatics group, Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, Croatia.,School of Bioscience, University of Skövde, Skövde, Sweden
| | - Ivan Mijakovic
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.,The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| |
Collapse
|
10
|
Abstract
The complexome of a cell is the entirety of its complexes. Complexome capture studies have mostly focused on protein-protein interactions, which has left a gap in our knowledge of the global interactions of RNAs. To overcome these limitations, we recently introduced gradient profiling by sequencing (Grad-seq), which analyzes in a high-throughput fashion soluble cellular complexes after their separation in a glycerol gradient by fraction-wise RNA-seq and mass spectrometry. Here, we describe a detailed Grad-seq protocol for Streptococcus pneumoniae, which should also be applicable to other bacterial species.
Collapse
Affiliation(s)
- Jens Hör
- Institute of Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Jörg Vogel
- Institute of Molecular Infection Biology, University of Würzburg, Würzburg, Germany.
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany.
| |
Collapse
|
11
|
Schäkermann S, Wüllner D, Yayci A, Emili A, Bandow JE. Applicability of Chromatographic Co-Elution for Antibiotic Target Identification. Proteomics 2020; 21:e2000038. [PMID: 32951352 DOI: 10.1002/pmic.202000038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 09/09/2020] [Indexed: 11/07/2022]
Abstract
Identification of the molecular target is a crucial step in evaluating novel antibiotics. To support target identification, a label-free method based on chromatographic co-elution has previously been developed. Target identification by chromatographic coelution (TICC) exploits the alteration of the elution profile of target-bound drug versus free drug in ion exchange (IEX) chromatography to identify potential target proteins from elution fractions. The applicability of TICC for antibiotic research is investigated by evaluating which proteins, that is, putative targets, can be monitored in Bacillus subtilis. Coelution of components of known protein complexes provides a read-out for how well the native state of proteins is conserved during chromatography. Rifampicin, which targets RNA polymerase, is used in a proof-of-concept study.
Collapse
Affiliation(s)
- Sina Schäkermann
- Applied Microbiology, Faculty of Biology and Biotechnology, Ruhr-Universität Bochum, 44801, Bochum, Germany
| | - Dominik Wüllner
- Applied Microbiology, Faculty of Biology and Biotechnology, Ruhr-Universität Bochum, 44801, Bochum, Germany
| | - Abdulkadir Yayci
- Applied Microbiology, Faculty of Biology and Biotechnology, Ruhr-Universität Bochum, 44801, Bochum, Germany
| | - Andrew Emili
- Center for Network Systems Biology, Boston University School of Medicine, Boston, MA, 02215, USA
| | - Julia Elisabeth Bandow
- Applied Microbiology, Faculty of Biology and Biotechnology, Ruhr-Universität Bochum, 44801, Bochum, Germany
| |
Collapse
|
12
|
M B, P C. Comparative analysis of differential proteome-wide protein-protein interaction network of Methanobrevibacter ruminantium M1. Biochem Biophys Rep 2019; 20:100698. [PMID: 31763465 PMCID: PMC6859225 DOI: 10.1016/j.bbrep.2019.100698] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 10/12/2019] [Accepted: 10/14/2019] [Indexed: 11/22/2022] Open
Abstract
A proteome-wide protein-protein interaction (PPI) network of Methanobrevibacter ruminantium M1 (MRU), a predominant rumen methanogen, was constructed from its metabolic genes using a gene neighborhood algorithm and then compared with closely related rumen methanogens Using proteome-wide PPI approach, we constructed network encompassed 2194 edges and 637 nodes interacting with 634 genes. Network quality and robustness of functional modules were assessed with gene ontology terms. A structure-function-metabolism mapping for each protein has been carried out with efforts to extract experimental PPI concomitant information from the literature. The results of our study revealed that some topological properties of its network were robust for sharing homologous protein interactions across heterotrophic and hydrogenotrophic methanogens. MRU proteome has shown to establish many PPI sub-networks for associated metabolic subsystems required to survive in the rumen environment. MRU genome found to share interacting proteins from its PPI network involved in specific metabolic subsystems distinct to heterotrophic and hydrogenotrophic methanogens. Across these proteomes, the interacting proteins from differential PPI networks were shared in common for the biosynthesis of amino acids, nucleosides, and nucleotides and energy metabolism in which more fractions of protein pairs shared with Methanosarcina acetivorans. Our comparative study expedites our knowledge to understand a complex proteome network associated with typical metabolic subsystems of MRU and to improve its genome-scale reconstruction in the future.
Collapse
Affiliation(s)
| | - Chellapandi P
- Molecular Systems Engineering Lab, Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli, 620 024, Tamil Nadu, India
| |
Collapse
|
13
|
Prathiviraj R, Berchmans S, Chellapandi P. Analysis of modularity in proteome-wide protein interaction networks of Methanothermobacter thermautotrophicus strain ΔH and metal-loving bacteria. ACTA ACUST UNITED AC 2019. [DOI: 10.1007/s42485-019-00019-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
|
14
|
Mercy C, Ducret A, Slager J, Lavergne JP, Freton C, Nagarajan SN, Garcia PS, Noirot-Gros MF, Dubarry N, Nourikyan J, Veening JW, Grangeasse C. RocS drives chromosome segregation and nucleoid protection in Streptococcus pneumoniae. Nat Microbiol 2019; 4:1661-1670. [PMID: 31182798 DOI: 10.1038/s41564-019-0472-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 04/26/2019] [Indexed: 11/09/2022]
Abstract
Chromosome segregation in bacteria is poorly understood outside some prominent model strains1-5 and even less is known about how it is coordinated with other cellular processes. This is the case for the opportunistic human pathogen Streptococcus pneumoniae (the pneumococcus)6, which lacks the Min and the nucleoid occlusion systems7, and possesses only an incomplete chromosome partitioning Par(A)BS system, in which ParA is absent8. The bacterial tyrosine kinase9 CpsD, which is required for capsule production, was previously found to interfere with chromosome segregation10. Here, we identify a protein of unknown function that interacts with CpsD and drives chromosome segregation. RocS (Regulator of Chromosome Segregation) is a membrane-bound protein that interacts with both DNA and the chromosome partitioning protein ParB to properly segregate the origin of replication region to new daughter cells. In addition, we show that RocS interacts with the cell division protein FtsZ and hinders cell division. Altogether, this work reveals that RocS is the cornerstone of a nucleoid protection system ensuring proper chromosome segregation and cell division in coordination with the biogenesis of the protective capsular layer.
Collapse
Affiliation(s)
- Chryslène Mercy
- Molecular Microbiology and Structural Biochemistry, UMR 5086, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique, Lyon, France
| | - Adrien Ducret
- Molecular Microbiology and Structural Biochemistry, UMR 5086, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique, Lyon, France
| | - Jelle Slager
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic Biology, University of Groningen, Groningen, The Netherlands
| | - Jean-Pierre Lavergne
- Molecular Microbiology and Structural Biochemistry, UMR 5086, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique, Lyon, France
| | - Céline Freton
- Molecular Microbiology and Structural Biochemistry, UMR 5086, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique, Lyon, France
| | - Sathya Narayanan Nagarajan
- Molecular Microbiology and Structural Biochemistry, UMR 5086, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique, Lyon, France
| | - Pierre Simon Garcia
- Molecular Microbiology and Structural Biochemistry, UMR 5086, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique, Lyon, France
| | - Marie-Francoise Noirot-Gros
- Micalis Institute, UMR1319, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France.,Biosciences Division, Argonne National Laboratory, Lemont, IL, USA
| | - Nelly Dubarry
- Molecular Microbiology and Structural Biochemistry, UMR 5086, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique, Lyon, France.,Evotec ID, Marcy l'Etoile, France
| | - Julien Nourikyan
- Molecular Microbiology and Structural Biochemistry, UMR 5086, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique, Lyon, France
| | - Jan-Willem Veening
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic Biology, University of Groningen, Groningen, The Netherlands.,Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Biophore Building, Lausanne, Switzerland
| | - Christophe Grangeasse
- Molecular Microbiology and Structural Biochemistry, UMR 5086, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique, Lyon, France.
| |
Collapse
|
15
|
Hao T, Zhao L, Wu D, Wang B, Feng X, Wang E, Sun J. The Protein-Protein Interaction Network of Litopenaeus vannamei Haemocytes. Front Physiol 2019; 10:156. [PMID: 30863321 PMCID: PMC6399580 DOI: 10.3389/fphys.2019.00156] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 02/08/2019] [Indexed: 12/23/2022] Open
Abstract
Protein–protein interaction networks (PINs) have been constructed in various organisms and utilized to conduct evolutionary analyses and functional predictions. Litopenaeus vannamei is a high-valued commercial aquaculture species with an uncharacterized interactome. With the development of RNA-seq techniques and systems biology, it is possible to obtain genome-wide transcriptional information for L. vannamei and construct a systematic network based on these data. In this work, based on the RNA-seq of haemocytes we constructed the first L. vannamei PIN including 4,858 proteins and 104,187 interactions. The PIN constructed here is the first large-scale PIN for shrimp. The confidence scores of interactions in the PIN were evaluated on the basis of sequence homology and genetic relationships. The immune-specific sub-network was extracted from global PIN, and more than a third of proteins were found in signaling pathways in the sub-network, which indicates an inseparable relationship between signaling processes and immune mechanisms. Six selected signaling pathways were constructed at different age groups based on evolutionary analyses. Furthermore, we showed that the functions of the pathways’ proteins were associated with their evolutionary history based on the evolutionary analyses combining with protein functional analyses. In addition, the functions of 1,955 unclassified proteins which were associated with 3,191 unigenes were assigned using the PIN, which account for approximately 70.3 and 44.9% of the previously unclassified proteins and unigenes in the network, respectively. The annotation of unclassified proteins and unigenes based on the PIN provides new candidates for further functional studies. The immune-specific sub-network and the pathways extracted from the PIN provide a novel information source for studying of immune mechanisms and disease resistances in shrimp.
Collapse
Affiliation(s)
- Tong Hao
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin, China
| | - Lingxuan Zhao
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin, China
| | - Dan Wu
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin, China
| | - Bin Wang
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin, China
| | - Xin Feng
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin, China
| | - Edwin Wang
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin, China.,Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Jinsheng Sun
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin, China
| |
Collapse
|
16
|
Carro L. Protein-protein interactions in bacteria: a promising and challenging avenue towards the discovery of new antibiotics. Beilstein J Org Chem 2018; 14:2881-2896. [PMID: 30546472 PMCID: PMC6278769 DOI: 10.3762/bjoc.14.267] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 11/02/2018] [Indexed: 12/11/2022] Open
Abstract
Antibiotics are potent pharmacological weapons against bacterial infections; however, the growing antibiotic resistance of microorganisms is compromising the efficacy of the currently available pharmacotherapies. Even though antimicrobial resistance is not a new problem, antibiotic development has failed to match the growth of resistant pathogens and hence, it is highly critical to discover new anti-infective drugs with novel mechanisms of action which will help reducing the burden of multidrug-resistant microorganisms. Protein–protein interactions (PPIs) are involved in a myriad of vital cellular processes and have become an attractive target to treat diseases. Therefore, targeting PPI networks in bacteria may offer a new and unconventional point of intervention to develop novel anti-infective drugs which can combat the ever-increasing rate of multidrug-resistant bacteria. This review describes the progress achieved towards the discovery of molecules that disrupt PPI systems in bacteria for which inhibitors have been identified and whose targets could represent an alternative lead discovery strategy to obtain new anti-infective molecules.
Collapse
Affiliation(s)
- Laura Carro
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| |
Collapse
|
17
|
Wuchty S, Müller SA, Caufield JH, Häuser R, Aloy P, Kalkhof S, Uetz P. Proteome Data Improves Protein Function Prediction in the Interactome of Helicobacter pylori. Mol Cell Proteomics 2018; 17:961-973. [PMID: 29414760 DOI: 10.1074/mcp.ra117.000474] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 01/25/2018] [Indexed: 01/17/2023] Open
Abstract
Helicobacter pylori is a common pathogen that is estimated to infect half of the human population, causing several diseases such as duodenal ulcer. Despite one of the first pathogens to be sequenced, its proteome remains poorly characterized as about one-third of its proteins have no functional annotation. Here, we integrate and analyze known protein interactions with proteomic and genomic data from different sources. We find that proteins with similar abundances tend to interact. Such an observation is accompanied by a trend of interactions to appear between proteins of similar functions, although some show marked cross-talk to others. Protein function prediction with protein interactions is significantly improved when interactions from other bacteria are included in our network, allowing us to obtain putative functions of more than 300 poorly or previously uncharacterized proteins. Proteins that are critical for the topological controllability of the underlying network are significantly enriched with genes that are up-regulated in the spiral compared with the coccoid form of H. pylori Determining their evolutionary conservation, we present evidence that 80 protein complexes are identical in composition with their counterparts in Escherichia coli, while 85 are partially conserved and 120 complexes are completely absent. Furthermore, we determine network clusters that coincide with related functions, gene essentiality, genetic context, cellular localization, and gene expression in different cellular states.
Collapse
Affiliation(s)
- Stefan Wuchty
- From the ‡Dept. of Computer Science.,§Center for Computational Science.,¶Dept. of Biology.,‖Sylvester Comprehensive Cancer Center, Univ. of Miami, Miami, FL 33156
| | - Stefan A Müller
- **German Center for Neurodegenerative Diseases (DZNE), 81377 Munich, Germany
| | - J Harry Caufield
- ‡‡Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VI 23284
| | - Roman Häuser
- §§German Cancer Research Center, 69120 Heidelberg, Germany
| | - Patrick Aloy
- ¶¶Joint IRB-BSC-CRG Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona) and the Barcelona Institute of Science and Technology. Barcelona, Catalonia, Spain.,‖‖Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain
| | - Stefan Kalkhof
- Department of Molecular Systems Biology, UFZ, Helmholtz-Centre for Environmental Research Leipzig, 04318 Leipzig, Germany.,Institute of Bioanalysis, University of Applied Sciences and Arts of Coburg, Friedrich-Streib-Str. 2, 96450 Coburg, Germany.,Fraunhofer Institute for Cell Therapy and Immunology, Department of Therapy Validation, 04103 Leipzig, Germany
| | - Peter Uetz
- ‡‡Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VI 23284
| |
Collapse
|
18
|
Abstract
More than 5 decades of work support the idea that cell envelope synthesis, including the inward growth of cell division, is tightly coordinated with DNA replication and protein synthesis through central metabolism. Remarkably, no unifying model exists to account for how these fundamentally disparate processes are functionally coupled. Recent studies demonstrate that proteins involved in carbohydrate and nitrogen metabolism can moonlight as direct regulators of cell division, coordinate cell division and DNA replication, and even suppress defects in DNA replication. In this minireview, we focus on studies illustrating the intimate link between metabolism and regulation of peptidoglycan (PG) synthesis during growth and division, and we identify the following three recurring themes. (i) Nutrient availability, not growth rate, is the primary determinant of cell size. (ii) The degree of gluconeogenic flux is likely to have a profound impact on the metabolites available for cell envelope synthesis, so growth medium selection is a critical consideration when designing and interpreting experiments related to morphogenesis. (iii) Perturbations in pathways relying on commonly shared and limiting metabolites, like undecaprenyl phosphate (Und-P), can lead to pleotropic phenotypes in unrelated pathways.
Collapse
|
19
|
Wuchty S, Rajagopala SV, Blazie SM, Parrish JR, Khuri S, Finley RL, Uetz P. The Protein Interactome of Streptococcus pneumoniae and Bacterial Meta-interactomes Improve Function Predictions. mSystems 2017; 2:e00019-17. [PMID: 28744484 PMCID: PMC5513735 DOI: 10.1128/msystems.00019-17] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 05/11/2017] [Indexed: 01/01/2023] Open
Abstract
The functions of roughly a third of all proteins in Streptococcus pneumoniae, a significant human-pathogenic bacterium, are unknown. Using a yeast two-hybrid approach, we have determined more than 2,000 novel protein interactions in this organism. We augmented this network with meta-interactome data that we defined as the pool of all interactions between evolutionarily conserved proteins in other bacteria. We found that such interactions significantly improved our ability to predict a protein's function, allowing us to provide functional predictions for 299 S. pneumoniae proteins with previously unknown functions. IMPORTANCE Identification of protein interactions in bacterial species can help define the individual roles that proteins play in cellular pathways and pathogenesis. Very few protein interactions have been identified for the important human pathogen S. pneumoniae. We used an experimental approach to identify over 2,000 new protein interactions for S. pneumoniae, the most extensive interactome data for this bacterium to date. To predict protein function, we used our interactome data augmented with interactions from other closely related bacteria. The combination of the experimental data and meta-interactome data significantly improved the prediction results, allowing us to assign possible functions to a large number of poorly characterized proteins.
Collapse
Affiliation(s)
- S. Wuchty
- Department of Computer Science, University of Miami, Coral Gables, Florida, USA
- Center for Computational Science, University of Miami, Coral Gables, Florida, USA
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, Florida, USA
- Department of Biology, University of Miami, Coral Gables, Florida, USA
| | | | - S. M. Blazie
- J Craig Venter Institute, Rockville, Maryland, USA
| | - J. R. Parrish
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - S. Khuri
- Department of Computer Science, University of Miami, Coral Gables, Florida, USA
- Center for Computational Science, University of Miami, Coral Gables, Florida, USA
| | - R. L. Finley
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - P. Uetz
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, Virginia, USA
| |
Collapse
|
20
|
Liu Y, Li J, Du G, Chen J, Liu L. Metabolic engineering of Bacillus subtilis fueled by systems biology: Recent advances and future directions. Biotechnol Adv 2017; 35:20-30. [DOI: 10.1016/j.biotechadv.2016.11.003] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 10/21/2016] [Accepted: 11/16/2016] [Indexed: 12/25/2022]
|
21
|
Reconstruction and Application of Protein-Protein Interaction Network. Int J Mol Sci 2016; 17:ijms17060907. [PMID: 27338356 PMCID: PMC4926441 DOI: 10.3390/ijms17060907] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2016] [Revised: 05/31/2016] [Accepted: 06/03/2016] [Indexed: 11/17/2022] Open
Abstract
The protein-protein interaction network (PIN) is a useful tool for systematic investigation of the complex biological activities in the cell. With the increasing interests on the proteome-wide interaction networks, PINs have been reconstructed for many species, including virus, bacteria, plants, animals, and humans. With the development of biological techniques, the reconstruction methods of PIN are further improved. PIN has gradually penetrated many fields in biological research. In this work we systematically reviewed the development of PIN in the past fifteen years, with respect to its reconstruction and application of function annotation, subsystem investigation, evolution analysis, hub protein analysis, and regulation mechanism analysis. Due to the significant role of PIN in the in-depth exploration of biological process mechanisms, PIN will be preferred by more and more researchers for the systematic study of the protein systems in various kinds of organisms.
Collapse
|
22
|
Shatsky M, Dong M, Liu H, Yang LL, Choi M, Singer ME, Geller JT, Fisher SJ, Hall SC, Hazen TC, Brenner SE, Butland G, Jin J, Witkowska HE, Chandonia JM, Biggin MD. Quantitative Tagless Copurification: A Method to Validate and Identify Protein-Protein Interactions. Mol Cell Proteomics 2016; 15:2186-202. [PMID: 27099342 PMCID: PMC5083090 DOI: 10.1074/mcp.m115.057117] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Indexed: 01/18/2023] Open
Abstract
Identifying protein-protein interactions (PPIs) at an acceptable false discovery rate (FDR) is challenging. Previously we identified several hundred PPIs from affinity purification - mass spectrometry (AP-MS) data for the bacteria Escherichia coli and Desulfovibrio vulgaris. These two interactomes have lower FDRs than any of the nine interactomes proposed previously for bacteria and are more enriched in PPIs validated by other data than the nine earlier interactomes. To more thoroughly determine the accuracy of ours or other interactomes and to discover further PPIs de novo, here we present a quantitative tagless method that employs iTRAQ MS to measure the copurification of endogenous proteins through orthogonal chromatography steps. 5273 fractions from a four-step fractionation of a D. vulgaris protein extract were assayed, resulting in the detection of 1242 proteins. Protein partners from our D. vulgaris and E. coli AP-MS interactomes copurify as frequently as pairs belonging to three benchmark data sets of well-characterized PPIs. In contrast, the protein pairs from the nine other bacterial interactomes copurify two- to 20-fold less often. We also identify 200 high confidence D. vulgaris PPIs based on tagless copurification and colocalization in the genome. These PPIs are as strongly validated by other data as our AP-MS interactomes and overlap with our AP-MS interactome for D.vulgaris within 3% of expectation, once FDRs and false negative rates are taken into account. Finally, we reanalyzed data from two quantitative tagless screens of human cell extracts. We estimate that the novel PPIs reported in these studies have an FDR of at least 85% and find that less than 7% of the novel PPIs identified in each screen overlap. Our results establish that a quantitative tagless method can be used to validate and identify PPIs, but that such data must be analyzed carefully to minimize the FDR.
Collapse
Affiliation(s)
- Maxim Shatsky
- From the ‡Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Ming Dong
- §Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Haichuan Liu
- ¶OB/GYN Department, University of California San Francisco-Sandler-Moore Mass Spectrometry Core Facility, University of California, San Francisco, California 94143
| | - Lee Lisheng Yang
- ‖Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Megan Choi
- §Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Mary E Singer
- **Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Jil T Geller
- **Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Susan J Fisher
- ¶OB/GYN Department, University of California San Francisco-Sandler-Moore Mass Spectrometry Core Facility, University of California, San Francisco, California 94143
| | - Steven C Hall
- ¶OB/GYN Department, University of California San Francisco-Sandler-Moore Mass Spectrometry Core Facility, University of California, San Francisco, California 94143
| | - Terry C Hazen
- ‡‡Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee 37996; §§Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Steven E Brenner
- From the ‡Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720; ¶¶Department of Plant and Microbial Biology, University of California, Berkeley, California 94720
| | - Gareth Butland
- ‖‖Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Jian Jin
- ‖Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - H Ewa Witkowska
- ¶OB/GYN Department, University of California San Francisco-Sandler-Moore Mass Spectrometry Core Facility, University of California, San Francisco, California 94143
| | - John-Marc Chandonia
- From the ‡Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720;
| | - Mark D Biggin
- §Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720;
| |
Collapse
|
23
|
Garcia-Garcia T, Poncet S, Derouiche A, Shi L, Mijakovic I, Noirot-Gros MF. Role of Protein Phosphorylation in the Regulation of Cell Cycle and DNA-Related Processes in Bacteria. Front Microbiol 2016; 7:184. [PMID: 26909079 PMCID: PMC4754617 DOI: 10.3389/fmicb.2016.00184] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 02/02/2016] [Indexed: 11/26/2022] Open
Abstract
In all living organisms, the phosphorylation of proteins modulates various aspects of their functionalities. In eukaryotes, protein phosphorylation plays a key role in cell signaling, gene expression, and differentiation. Protein phosphorylation is also involved in the global control of DNA replication during the cell cycle, as well as in the mechanisms that cope with stress-induced replication blocks. Similar to eukaryotes, bacteria use Hanks-type kinases and phosphatases for signal transduction, and protein phosphorylation is involved in numerous cellular processes. However, it remains unclear whether protein phosphorylation in bacteria can also regulate the activity of proteins involved in DNA-mediated processes such as DNA replication or repair. Accumulating evidence supported by functional and biochemical studies suggests that phospho-regulatory mechanisms also take place during the bacterial cell cycle. Recent phosphoproteomics and interactomics studies identified numerous phosphoproteins involved in various aspect of DNA metabolism strongly supporting the existence of such level of regulation in bacteria. Similar to eukaryotes, bacterial scaffolding-like proteins emerged as platforms for kinase activation and signaling. This review reports the current knowledge on the phosphorylation of proteins involved in the maintenance of genome integrity and the regulation of cell cycle in bacteria that reveals surprising similarities to eukaryotes.
Collapse
Affiliation(s)
| | - Sandrine Poncet
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay Jouy-en-Josas, France
| | - Abderahmane Derouiche
- Systems and Synthetic Biology, Department of Chemical and Biological Engineering, Chalmers University of Technology Gothenburg, Sweden
| | - Lei Shi
- Systems and Synthetic Biology, Department of Chemical and Biological Engineering, Chalmers University of Technology Gothenburg, Sweden
| | - Ivan Mijakovic
- Systems and Synthetic Biology, Department of Chemical and Biological Engineering, Chalmers University of TechnologyGothenburg, Sweden; Novo Nordisk Foundation Center for Biosustainability, Technical University of DenmarkHørsholm, Denmark
| | | |
Collapse
|
24
|
Shatsky M, Allen S, Gold BL, Liu NL, Juba TR, Reveco SA, Elias DA, Prathapam R, He J, Yang W, Szakal ED, Liu H, Singer ME, Geller JT, Lam BR, Saini A, Trotter VV, Hall SC, Fisher SJ, Brenner SE, Chhabra SR, Hazen TC, Wall JD, Witkowska HE, Biggin MD, Chandonia JM, Butland G. Bacterial Interactomes: Interacting Protein Partners Share Similar Function and Are Validated in Independent Assays More Frequently Than Previously Reported. Mol Cell Proteomics 2016; 15:1539-55. [PMID: 26873250 DOI: 10.1074/mcp.m115.054692] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Indexed: 01/31/2023] Open
Abstract
Numerous affinity purification-mass spectrometry (AP-MS) and yeast two-hybrid screens have each defined thousands of pairwise protein-protein interactions (PPIs), most of which are between functionally unrelated proteins. The accuracy of these networks, however, is under debate. Here, we present an AP-MS survey of the bacterium Desulfovibrio vulgaris together with a critical reanalysis of nine published bacterial yeast two-hybrid and AP-MS screens. We have identified 459 high confidence PPIs from D. vulgaris and 391 from Escherichia coli Compared with the nine published interactomes, our two networks are smaller, are much less highly connected, and have significantly lower false discovery rates. In addition, our interactomes are much more enriched in protein pairs that are encoded in the same operon, have similar functions, and are reproducibly detected in other physical interaction assays than the pairs reported in prior studies. Our work establishes more stringent benchmarks for the properties of protein interactomes and suggests that bona fide PPIs much more frequently involve protein partners that are annotated with similar functions or that can be validated in independent assays than earlier studies suggested.
Collapse
Affiliation(s)
- Maxim Shatsky
- From the Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720
| | - Simon Allen
- the Department of Obstetrics, Gynecology and Reproductive Sciences and Sandler-Moore Mass Spectrometry Core Facility, University of California at San Francisco, San Francisco, California, 94143
| | - Barbara L Gold
- the Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720
| | - Nancy L Liu
- the Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720
| | - Thomas R Juba
- the Departments of Biochemistry and of Molecular Microbiology and Immunology, University of Missouri, Columbia, Missouri, 65211
| | - Sonia A Reveco
- From the Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720
| | - Dwayne A Elias
- the Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, 37831
| | - Ramadevi Prathapam
- the Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720
| | - Jennifer He
- the Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720
| | - Wenhong Yang
- the Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720
| | - Evelin D Szakal
- the Department of Obstetrics, Gynecology and Reproductive Sciences and Sandler-Moore Mass Spectrometry Core Facility, University of California at San Francisco, San Francisco, California, 94143
| | - Haichuan Liu
- the Department of Obstetrics, Gynecology and Reproductive Sciences and Sandler-Moore Mass Spectrometry Core Facility, University of California at San Francisco, San Francisco, California, 94143
| | - Mary E Singer
- the Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720
| | - Jil T Geller
- the Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720
| | - Bonita R Lam
- the Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720
| | - Avneesh Saini
- the Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720
| | - Valentine V Trotter
- the Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720
| | - Steven C Hall
- the Department of Obstetrics, Gynecology and Reproductive Sciences and Sandler-Moore Mass Spectrometry Core Facility, University of California at San Francisco, San Francisco, California, 94143
| | - Susan J Fisher
- the Department of Obstetrics, Gynecology and Reproductive Sciences and Sandler-Moore Mass Spectrometry Core Facility, University of California at San Francisco, San Francisco, California, 94143
| | - Steven E Brenner
- From the Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720; the Department of Plant and Microbial Biology, University of California at Berkeley, Berkeley, California, 94720
| | - Swapnil R Chhabra
- From the Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720
| | - Terry C Hazen
- the Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee, 37996; and
| | - Judy D Wall
- the Departments of Biochemistry and of Molecular Microbiology and Immunology, University of Missouri, Columbia, Missouri, 65211
| | - H Ewa Witkowska
- the Department of Obstetrics, Gynecology and Reproductive Sciences and Sandler-Moore Mass Spectrometry Core Facility, University of California at San Francisco, San Francisco, California, 94143
| | - Mark D Biggin
- the Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720
| | - John-Marc Chandonia
- From the Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720;
| | - Gareth Butland
- the Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720; From the Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720;
| |
Collapse
|
25
|
Michna RH, Zhu B, Mäder U, Stülke J. SubtiWiki 2.0--an integrated database for the model organism Bacillus subtilis. Nucleic Acids Res 2015; 44:D654-62. [PMID: 26433225 PMCID: PMC4702770 DOI: 10.1093/nar/gkv1006] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 09/23/2015] [Indexed: 12/31/2022] Open
Abstract
To understand living cells, we need knowledge of each of their parts as well as about the interactions of these parts. To gain rapid and comprehensive access to this information, annotation databases are required. Here, we present SubtiWiki 2.0, the integrated database for the model bacterium Bacillus subtilis (http://subtiwiki.uni-goettingen.de/). SubtiWiki provides text-based access to published information about the genes and proteins of B. subtilis as well as presentations of metabolic and regulatory pathways. Moreover, manually curated protein-protein interactions diagrams are linked to the protein pages. Finally, expression data are shown with respect to gene expression under 104 different conditions as well as absolute protein quantification for cytoplasmic proteins. To facilitate the mobile use of SubtiWiki, we have now expanded it by Apps that are available for iOS and Android devices. Importantly, the App allows to link private notes and pictures to the gene/protein pages. Today, SubtiWiki has become one of the most complete collections of knowledge on a living organism in one single resource.
Collapse
Affiliation(s)
- Raphael H Michna
- Department of General Microbiology, Institute of Microbiology and Genetics, Georg-August University Göttingen, Grisebachstr. 8, D-37077 Göttingen, Germany
| | - Bingyao Zhu
- Department of General Microbiology, Institute of Microbiology and Genetics, Georg-August University Göttingen, Grisebachstr. 8, D-37077 Göttingen, Germany
| | - Ulrike Mäder
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Jahnstr. 15a, D-17475 Greifswald, Germany
| | - Jörg Stülke
- Department of General Microbiology, Institute of Microbiology and Genetics, Georg-August University Göttingen, Grisebachstr. 8, D-37077 Göttingen, Germany
| |
Collapse
|
26
|
MreB-Dependent Inhibition of Cell Elongation during the Escape from Competence in Bacillus subtilis. PLoS Genet 2015; 11:e1005299. [PMID: 26091431 PMCID: PMC4474612 DOI: 10.1371/journal.pgen.1005299] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 05/26/2015] [Indexed: 02/02/2023] Open
Abstract
During bacterial exponential growth, the morphogenetic actin-like MreB proteins form membrane-associated assemblies that move processively following trajectories perpendicular to the long axis of the cell. Such MreB structures are thought to scaffold and restrict the movement of peptidoglycan synthesizing machineries, thereby coordinating sidewall elongation. In Bacillus subtilis, this function is performed by the redundant action of three MreB isoforms, namely MreB, Mbl and MreBH. mreB and mbl are highly transcribed from vegetative promoters. We have found that their expression is maximal at the end of exponential phase, and rapidly decreases to a low basal level upon entering stationary phase. However, in cells developing genetic competence, a stationary phase physiological adaptation, expression of mreB was specifically reactivated by the central competence regulator ComK. In competent cells, MreB was found in complex with several competence proteins by in vitro pull-down assays. In addition, it co-localized with the polar clusters formed by the late competence peripheral protein ComGA, in a ComGA-dependent manner. ComGA has been shown to be essential for the inhibition of cell elongation characteristic of cells escaping the competence state. We show here that the pathway controlling this elongation inhibition also involves MreB. Our findings suggest that ComGA sequesters MreB to prevent cell elongation and therefore the escape from competence. In bacterial cells, like in their eukaryotic counterparts, precise spatiotemporal localization of proteins is critical for their cellular function. This study shows that the expression and the localization of the bacterial actin-like MreB protein are growth phase-dependent. During exponential growth, we previously showed that MreB, together with other morphogenetic factors, forms discrete assemblies that move in a directed manner along peripheral tracks. Here, we demonstrate that in cells that develop genetic competence during stationary phase, transcription of mreB is specifically activated and MreB relocalizes to the cell poles. Our findings suggest a model in which MreB sequestration by the late competence protein ComGA prevents cell elongation during the escape from competence.
Collapse
|
27
|
Detert Oude Weme RGJ, Kovács ÁT, de Jong SJG, Veening JW, Siebring J, Kuipers OP. Single cell FRET analysis for the identification of optimal FRET-pairs in Bacillus subtilis using a prototype MEM-FLIM system. PLoS One 2015; 10:e0123239. [PMID: 25886351 PMCID: PMC4401445 DOI: 10.1371/journal.pone.0123239] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 03/01/2015] [Indexed: 11/21/2022] Open
Abstract
Protein-protein interactions can be studied in vitro, e.g. with bacterial or yeast two-hybrid systems or surface plasmon resonance. In contrast to in vitro techniques, in vivo studies of protein-protein interactions allow examination of spatial and temporal behavior of such interactions in their native environment. One approach to study protein-protein interactions in vivo is via Förster Resonance Energy Transfer (FRET). Here, FRET efficiency of selected FRET-pairs was studied at the single cell level using sensitized emission and Frequency Domain-Fluorescence Lifetime Imaging Microscopy (FD-FLIM). For FRET-FLIM, a prototype Modulated Electron-Multiplied FLIM system was used, which is, to the best of our knowledge, the first account of Frequency Domain FLIM to analyze FRET in single bacterial cells. To perform FRET-FLIM, we first determined and benchmarked the best fluorescent protein-pair for FRET in Bacillus subtilis using a novel BglBrick-compatible integration vector. We show that GFP-tagRFP is an excellent donor-acceptor pair for B. subtilis in vivo FRET studies. As a proof of concept, selected donor and acceptor fluorescent proteins were fused using a linker that contained a tobacco etch virus (TEV)-protease recognition sequence. Induction of TEV-protease results in loss of FRET efficiency and increase in fluorescence lifetime. The loss of FRET efficiency after TEV induction can be followed in time in single cells via time-lapse microscopy. This work will facilitate future studies of in vivo dynamics of protein complexes in single B. subtilis cells.
Collapse
Affiliation(s)
- Ruud G. J. Detert Oude Weme
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic Biology, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Ákos T. Kovács
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic Biology, University of Groningen, 9747 AG Groningen, The Netherlands
| | | | - Jan-Willem Veening
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic Biology, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Jeroen Siebring
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic Biology, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Oscar P. Kuipers
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic Biology, University of Groningen, 9747 AG Groningen, The Netherlands
- * E-mail:
| |
Collapse
|
28
|
Subramanian N, Torabi-Parizi P, Gottschalk RA, Germain RN, Dutta B. Network representations of immune system complexity. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2015; 7:13-38. [PMID: 25625853 PMCID: PMC4339634 DOI: 10.1002/wsbm.1288] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Revised: 12/09/2014] [Accepted: 12/11/2014] [Indexed: 12/25/2022]
Abstract
The mammalian immune system is a dynamic multiscale system composed of a hierarchically organized set of molecular, cellular, and organismal networks that act in concert to promote effective host defense. These networks range from those involving gene regulatory and protein–protein interactions underlying intracellular signaling pathways and single‐cell responses to increasingly complex networks of in vivo cellular interaction, positioning, and migration that determine the overall immune response of an organism. Immunity is thus not the product of simple signaling events but rather nonlinear behaviors arising from dynamic, feedback‐regulated interactions among many components. One of the major goals of systems immunology is to quantitatively measure these complex multiscale spatial and temporal interactions, permitting development of computational models that can be used to predict responses to perturbation. Recent technological advances permit collection of comprehensive datasets at multiple molecular and cellular levels, while advances in network biology support representation of the relationships of components at each level as physical or functional interaction networks. The latter facilitate effective visualization of patterns and recognition of emergent properties arising from the many interactions of genes, molecules, and cells of the immune system. We illustrate the power of integrating ‘omics’ and network modeling approaches for unbiased reconstruction of signaling and transcriptional networks with a focus on applications involving the innate immune system. We further discuss future possibilities for reconstruction of increasingly complex cellular‐ and organism‐level networks and development of sophisticated computational tools for prediction of emergent immune behavior arising from the concerted action of these networks. WIREs Syst Biol Med 2015, 7:13–38. doi: 10.1002/wsbm.1288 This article is categorized under:
Analytical and Computational Methods > Computational Methods Laboratory Methods and Technologies > Macromolecular Interactions, Methods
Collapse
Affiliation(s)
- Naeha Subramanian
- Institute for Systems Biology, Seattle, WA, USA; Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | | | | | | | | |
Collapse
|
29
|
Gale P, Hill A, Kelly L, Bassett J, McClure P, Le Marc Y, Soumpasis I. Applications of omics approaches to the development of microbiological risk assessment using RNA virus dose-response models as a case study. J Appl Microbiol 2014; 117:1537-48. [PMID: 25269811 PMCID: PMC7166579 DOI: 10.1111/jam.12656] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 09/26/2014] [Indexed: 12/27/2022]
Abstract
T e in the amount of ‘omics’ data available and in our ability to interpret those data. The aim of this paper was to consider how omics techniques can be used to improve and refine microbiological risk assessment, using dose–response models for RNA viruses, with particular reference to norovirus through the oral route as the case study. The dose–response model for initial infection in the gastrointestinal tract is broken down into the component steps at the molecular level and the feasibility of assigning probabilities to each step assessed. The molecular mechanisms are not sufficiently well understood at present to enable quantitative estimation of probabilities on the basis of omics data. At present, the great strength of gene sequence data appears to be in giving information on the distribution and proportion of susceptible genotypes (for example due to the presence of the appropriate pathogen‐binding receptor) in the host population rather than in predicting specificities from the amino acid sequences concurrently obtained. The nature of the mutant spectrum in RNA viruses greatly complicates the application of omics approaches to the development of mechanistic dose–response models and prevents prediction of risks of disease progression (given infection has occurred) at the level of the individual host. However, molecular markers in the host and virus may enable more broad predictions to be made about the consequences of exposure in a population. In an alternative approach, comparing the results of deep sequencing of RNA viruses in the faeces/vomitus from donor humans with those from their infected recipients may enable direct estimates of the average probability of infection per virion to be made.
Collapse
Affiliation(s)
- P Gale
- Animal Health and Veterinary Laboratories Agency, Surrey, UK
| | | | | | | | | | | | | |
Collapse
|
30
|
Shi L, Pigeonneau N, Ventroux M, Derouiche A, Bidnenko V, Mijakovic I, Noirot-Gros MF. Protein-tyrosine phosphorylation interaction network in Bacillus subtilis reveals new substrates, kinase activators and kinase cross-talk. Front Microbiol 2014; 5:538. [PMID: 25374563 PMCID: PMC4205851 DOI: 10.3389/fmicb.2014.00538] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Accepted: 09/26/2014] [Indexed: 01/28/2023] Open
Abstract
Signal transduction in eukaryotes is generally transmitted through phosphorylation cascades that involve a complex interplay of transmembrane receptors, protein kinases, phosphatases and their targets. Our previous work indicated that bacterial protein-tyrosine kinases and phosphatases may exhibit similar properties, since they act on many different substrates. To capture the complexity of this phosphorylation-based network, we performed a comprehensive interactome study focused on the protein-tyrosine kinases and phosphatases in the model bacterium Bacillus subtilis. The resulting network identified many potential new substrates of kinases and phosphatases, some of which were experimentally validated. Our study highlighted the role of tyrosine and serine/threonine kinases and phosphatases in DNA metabolism, transcriptional control and cell division. This interaction network reveals significant crosstalk among different classes of kinases. We found that tyrosine kinases can bind to several modulators, transmembrane or cytosolic, consistent with a branching of signaling pathways. Most particularly, we found that the division site regulator MinD can form a complex with the tyrosine kinase PtkA and modulate its activity in vitro. In vivo, it acts as a scaffold protein which anchors the kinase at the cell pole. This network highlighted a role of tyrosine phosphorylation in the spatial regulation of the Z-ring during cytokinesis.
Collapse
Affiliation(s)
- Lei Shi
- Institut National de la Recherche Agronomique, UMR1319 Micalis Jouy-en-Josas, France ; Systems and Synthetic Biology, Department of Chemical and Biological Engineering, Chalmers University of Technology Gothenburg, Sweden
| | - Nathalie Pigeonneau
- Institut National de la Recherche Agronomique, UMR1319 Micalis Jouy-en-Josas, France
| | - Magali Ventroux
- Institut National de la Recherche Agronomique, UMR1319 Micalis Jouy-en-Josas, France
| | - Abderahmane Derouiche
- Institut National de la Recherche Agronomique, UMR1319 Micalis Jouy-en-Josas, France ; Systems and Synthetic Biology, Department of Chemical and Biological Engineering, Chalmers University of Technology Gothenburg, Sweden
| | - Vladimir Bidnenko
- Systems and Synthetic Biology, Department of Chemical and Biological Engineering, Chalmers University of Technology Gothenburg, Sweden
| | - Ivan Mijakovic
- Institut National de la Recherche Agronomique, UMR1319 Micalis Jouy-en-Josas, France ; Systems and Synthetic Biology, Department of Chemical and Biological Engineering, Chalmers University of Technology Gothenburg, Sweden
| | | |
Collapse
|
31
|
Huppert LA, Ramsdell TL, Chase MR, Sarracino DA, Fortune SM, Burton BM. The ESX system in Bacillus subtilis mediates protein secretion. PLoS One 2014; 9:e96267. [PMID: 24798022 PMCID: PMC4010439 DOI: 10.1371/journal.pone.0096267] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Accepted: 04/07/2014] [Indexed: 11/18/2022] Open
Abstract
Esat-6 protein secretion systems (ESX or Ess) are required for the virulence of several human pathogens, most notably Mycobacterium tuberculosis and Staphylococcus aureus. These secretion systems are defined by a conserved FtsK/SpoIIIE family ATPase and one or more WXG100 family secreted substrates. Gene clusters coding for ESX systems have been identified amongst many organisms including the highly tractable model system, Bacillus subtilis. In this study, we demonstrate that the B. subtilis yuk/yue locus codes for a nonessential ESX secretion system. We develop a functional secretion assay to demonstrate that each of the locus gene products is specifically required for secretion of the WXG100 virulence factor homolog, YukE. We then employ an unbiased approach to search for additional secreted substrates. By quantitative profiling of culture supernatants, we find that YukE may be the sole substrate that depends on the FtsK/SpoIIIE family ATPase for secretion. We discuss potential functional implications for secretion of a unique substrate.
Collapse
Affiliation(s)
- Laura A. Huppert
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Talia L. Ramsdell
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Michael R. Chase
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - David A. Sarracino
- Thermo Fisher Scientific, BRIMS Unit, Cambridge, Massachusetts, United States of America
| | - Sarah M. Fortune
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Briana M. Burton
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, United States of America
- * E-mail:
| |
Collapse
|
32
|
Hao T, Zeng Z, Wang B, Zhang Y, Liu Y, Geng X, Sun J. The protein-protein interaction network of eyestalk, Y-organ and hepatopancreas in Chinese mitten crab Eriocheir sinensis. BMC SYSTEMS BIOLOGY 2014; 8:39. [PMID: 24674293 PMCID: PMC3986667 DOI: 10.1186/1752-0509-8-39] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2014] [Accepted: 03/21/2014] [Indexed: 11/28/2022]
Abstract
Background The protein-protein interaction network (PIN) is an effective information tool for understanding the complex biological processes inside the cell and solving many biological problems such as signaling pathway identification and prediction of protein functions. Eriocheir sinensis is a highly-commercial aquaculture species with an unclear proteome background which hinders the construction and development of PIN for E. sinensis. However, in recent years, the development of next-generation deep-sequencing techniques makes it possible to get high throughput data of E. sinensis tanscriptome and subsequently obtain a systematic overview of the protein-protein interaction system. Results In this work we sequenced the transcriptional RNA of eyestalk, Y-organ and hepatopancreas in E. sinensis and generated a PIN of E. sinensis which included 3,223 proteins and 35,787 interactions. Each protein-protein interaction in the network was scored according to the homology and genetic relationship. The signaling sub-network, representing the signal transduction pathways in E. sinensis, was extracted from the global network, which depicted a global view of the signaling systems in E. sinensis. Seven basic signal transduction pathways were identified in E. sinensis. By investigating the evolution paths of the seven pathways, we found that these pathways got mature in different evolutionary stages. Moreover, the functions of unclassified proteins and unigenes in the PIN of E. sinensis were predicted. Specifically, the functions of 549 unclassified proteins related to 864 unclassified unigenes were assigned, which respectively covered 76% and 73% of all the unclassified proteins and unigenes in the network. Conclusions The PIN generated in this work is the first large-scale PIN of aquatic crustacean, thereby providing a paradigmatic blueprint of the aquatic crustacean interactome. Signaling sub-network extracted from the global PIN depicts the interaction of different signaling proteins and the evolutionary paths of the identified signal transduction pathways. Furthermore, the function assignment of unclassified proteins based on the PIN offers a new reference in protein function exploration. More importantly, the construction of the E. sinensis PIN provides necessary experience for the exploration of PINs in other aquatic crustacean species.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Jinsheng Sun
- Tianjin Key Laboratory of Animal and Plant Resistance/College of Life Science, Tianjin Normal University, Tianjin 300387, P,R, China.
| |
Collapse
|
33
|
Bacillus subtilis
Systems Biology: Applications of -Omics Techniques to the Study of Endospore Formation. Microbiol Spectr 2014; 2. [DOI: 10.1128/microbiolspec.tbs-0019-2013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
ABSTRACT
Endospore-forming bacteria, with
Bacillus subtilis
being the prevalent model organism, belong to the phylum Firmicutes. Although the last common ancestor of all
Firmicutes
is likely to have been an endospore-forming species, not every lineage in the phylum has maintained the ability to produce endospores (hereafter, spores). In 1997, the release of the full genome sequence for
B. subtilis
strain 168 marked the beginning of the genomic era for the study of spore formation (sporulation). In this original genome sequence, 139 of the 4,100 protein-coding genes were annotated as sporulation genes. By the time a revised genome sequence with updated annotations was published in 2009, that number had increased significantly, especially since transcriptional profiling studies (transcriptomics) led to the identification of several genes expressed under the control of known sporulation transcription factors. Over the past decade, genome sequences for multiple spore-forming species have been released (including several strains in the
Bacillus anthracis
/
Bacillus cereus
group and many
Clostridium
species), and phylogenomic analyses have revealed many conserved sporulation genes. Parallel advances in transcriptomics led to the identification of small untranslated regulatory RNAs (sRNAs), including some that are expressed during sporulation. An extended array of -omics techniques, i.e., techniques designed to probe gene function on a genome-wide scale, such as proteomics, metabolomics, and high-throughput protein localization studies, have been implemented in microbiology. Combined with the use of new computational methods for predicting gene function and inferring regulatory relationships on a global scale, these -omics approaches are uncovering novel information about sporulation and a variety of other bacterial cell processes.
Collapse
|
34
|
Häuser R, Ceol A, Rajagopala SV, Mosca R, Siszler G, Wermke N, Sikorski P, Schwarz F, Schick M, Wuchty S, Aloy P, Uetz P. A second-generation protein-protein interaction network of Helicobacter pylori. Mol Cell Proteomics 2014; 13:1318-29. [PMID: 24627523 DOI: 10.1074/mcp.o113.033571] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Helicobacter pylori infections cause gastric ulcers and play a major role in the development of gastric cancer. In 2001, the first protein interactome was published for this species, revealing over 1500 binary protein interactions resulting from 261 yeast two-hybrid screens. Here we roughly double the number of previously published interactions using an ORFeome-based, proteome-wide yeast two-hybrid screening strategy. We identified a total of 1515 protein-protein interactions, of which 1461 are new. The integration of all the interactions reported in H. pylori results in 3004 unique interactions that connect about 70% of its proteome. Excluding interactions of promiscuous proteins we derived from our new data a core network consisting of 908 interactions. We compared our data set to several other bacterial interactomes and experimentally benchmarked the conservation of interactions using 365 protein pairs (interologs) of E. coli of which one third turned out to be conserved in both species.
Collapse
Affiliation(s)
- Roman Häuser
- German Cancer Research Center (Deutsches Krebsforschungszentrum), Technologiepark 3, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
35
|
Cardenas PP, Gándara C, Alonso JC. DNA double strand break end-processing and RecA induce RecN expression levels in Bacillus subtilis. DNA Repair (Amst) 2013; 14:1-8. [PMID: 24373815 DOI: 10.1016/j.dnarep.2013.12.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Revised: 11/21/2013] [Accepted: 12/03/2013] [Indexed: 12/15/2022]
Abstract
Bacillus subtilis cells respond to double strand breaks (DSBs) with an ordered recruitment of repair proteins to the site lesion, being RecN one of the first responders. In B. subtilis, one of the responses to DSBs is to increase RecN expression rather than modifying its turnover rate. End-processing activities and the RecA protein itself contribute to increase RecN levels after DNA DSBs. RecO is required for RecA filament formation and full SOS induction, but its absence did not significantly affect RecN expression. Neither the absence of LexA nor the phosphorylation state of RecA or SsbA significantly affect RecN expression levels. These findings identify two major mechanisms (SOS and DSB response) used to respond to DSBs, with LexA required for one of them (SOS response). The DSB response, which requires end-processing and RecA or short RecO-independent RecA filaments, highlights the importance of guarding genome stability by modulating the DNA damage responses.
Collapse
Affiliation(s)
- Paula P Cardenas
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Darwin 3, 28049 Madrid, Spain
| | - Carolina Gándara
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Darwin 3, 28049 Madrid, Spain
| | - Juan C Alonso
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Darwin 3, 28049 Madrid, Spain.
| |
Collapse
|
36
|
Rueff AS, Chastanet A, Domínguez-Escobar J, Yao Z, Yates J, Prejean MV, Delumeau O, Noirot P, Wedlich-Söldner R, Filipe SR, Carballido-López R. An early cytoplasmic step of peptidoglycan synthesis is associated to MreB in Bacillus subtilis. Mol Microbiol 2013; 91:348-62. [PMID: 24261876 DOI: 10.1111/mmi.12467] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/18/2013] [Indexed: 12/23/2022]
Abstract
MreB proteins play a major role during morphogenesis of rod-shaped bacteria by organizing biosynthesis of the peptidoglycan cell wall. However, the mechanisms underlying this process are not well understood. In Bacillus subtilis, membrane-associated MreB polymers have been shown to be associated to elongation-specific complexes containing transmembrane morphogenetic factors and extracellular cell wall assembly proteins. We have now found that an early intracellular step of cell wall synthesis is also associated to MreB. We show that the previously uncharacterized protein YkuR (renamed DapI) is required for synthesis of meso-diaminopimelate (m-DAP), an essential constituent of the peptidoglycan precursor, and that it physically interacts with MreB. Highly inclined laminated optical sheet microscopy revealed that YkuR forms uniformly distributed foci that exhibit fast motion in the cytoplasm, and are not detected in cells lacking MreB. We propose a model in which soluble MreB organizes intracellular steps of peptidoglycan synthesis in the cytoplasm to feed the membrane-associated cell wall synthesizing machineries.
Collapse
Affiliation(s)
- Anne-Stéphanie Rueff
- INRA, UMR1319 Micalis, F-78352, Jouy-en-Josas, France; AgroParisTech, UMR1319 Micalis, F-78352, Jouy-en-Josas, France
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
37
|
Derouiche A, Bidnenko V, Grenha R, Pigonneau N, Ventroux M, Franz-Wachtel M, Nessler S, Noirot-Gros MF, Mijakovic I. Interaction of bacterial fatty-acid-displaced regulators with DNA is interrupted by tyrosine phosphorylation in the helix-turn-helix domain. Nucleic Acids Res 2013; 41:9371-81. [PMID: 23939619 PMCID: PMC3814354 DOI: 10.1093/nar/gkt709] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Bacteria possess transcription regulators (of the TetR family) specifically dedicated to repressing genes for cytochrome P450, involved in oxidation of polyunsaturated fatty acids. Interaction of these repressors with operator sequences is disrupted in the presence of fatty acids, and they are therefore known as fatty-acid-displaced regulators. Here, we describe a novel mechanism of inactivating the interaction of these proteins with DNA, illustrated by the example of Bacillus subtilis regulator FatR. FatR was found to interact in a two-hybrid assay with TkmA, an activator of the protein-tyrosine kinase PtkA. We show that FatR is phosphorylated specifically at the residue tyrosine 45 in its helix-turn-helix domain by the kinase PtkA. Structural modelling reveals that the hydroxyl group of tyrosine 45 interacts with DNA, and we show that this phosphorylation reduces FatR DNA binding capacity. Point mutants mimicking phosphorylation of FatR in vivo lead to a strong derepression of the fatR operon, indicating that this regulatory mechanism works independently of derepression by polyunsaturated fatty acids. Tyrosine 45 is a highly conserved residue, and PtkA from B. subtilis can phosphorylate FatR homologues from other bacteria. This indicates that phosphorylation of tyrosine 45 may be a general mechanism of switching off bacterial fatty-acid-displaced regulators.
Collapse
Affiliation(s)
- Abderahmane Derouiche
- INRA, UMR1319 Micalis, 78350 Jouy-en-Josas, France, Institut de Biochimie et Biophysique Moléculaire et Cellulaire, Université Paris-Sud 11, 91405 Orsay, France, Proteome Center Tübingen, University of Tübingen, 72076 Tübingen, Germany and Department of Chemical and Biological Engineering, Chalmers University of Technology, 41296 Gothenburg, Sweden
| | | | | | | | | | | | | | | | | |
Collapse
|
38
|
Monteferrante CG, MacKichan C, Marchadier E, Prejean MV, Carballido-López R, van Dijl JM. Mapping the twin-arginine protein translocation network of Bacillus subtilis. Proteomics 2013. [PMID: 23180473 DOI: 10.1002/pmic.201200416] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Bacteria employ twin-arginine translocation (Tat) pathways for the transport of folded proteins to extracytoplasmic destinations. In recent years, most studies on bacterial Tat pathways addressed the membrane-bound TatA(B)C subunits of the Tat translocase, and the specific interactions between this translocase and its substrate proteins. In contrast, relatively few studies investigated possible coactors in the TatA(B)C-dependent protein translocation process. The present studies were aimed at identifying interaction partners of the Tat pathway of Bacillus subtilis, which is a paradigm for studies on protein secretion by Gram-positive bacteria. Specifically, 36 interaction partners of the TatA and TatC subunits were identified by rigorous application of the yeast two-hybrid (Y2H) approach. Our Y2H analyses revealed that the three TatA isoforms of B. subtilis can form homo- and heterodimers. Subsequently, the secretion of the Tat substrates YwbN and PhoD was tested in mutant strains lacking genes for the TatAC interaction partners identified in our genome-wide Y2H screens. Our results show that the cell wall-bound protease WprA is important for YwbN secretion, and that the HemAT and CsbC proteins are required for PhoD secretion under phosphate starvation conditions. Taken together, our findings imply that the Bacillus Tat pathway is embedded in an intricate protein-protein interaction network.
Collapse
Affiliation(s)
- Carmine G Monteferrante
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | | | | | | | | | | |
Collapse
|
39
|
Durmuş Tekir SD, Ülgen KÖ. Systems biology of pathogen-host interaction: networks of protein-protein interaction within pathogens and pathogen-human interactions in the post-genomic era. Biotechnol J 2013; 8:85-96. [PMID: 23193100 PMCID: PMC7161785 DOI: 10.1002/biot.201200110] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Revised: 09/17/2012] [Accepted: 10/11/2012] [Indexed: 12/13/2022]
Abstract
Infectious diseases comprise some of the leading causes of death and disability worldwide. Interactions between pathogen and host proteins underlie the process of infection. Improved understanding of pathogen-host molecular interactions will increase our knowledge of the mechanisms involved in infection, and allow novel therapeutic solutions to be devised. Complete genome sequences for a number of pathogenic microorganisms, as well as the human host, has led to the revelation of their protein-protein interaction (PPI) networks. In this post-genomic era, pathogen-host interactions (PHIs) operating during infection can also be mapped. Detailed systematic analyses of PPI and PHI data together are required for a complete understanding of pathogenesis of infections. Here we review the striking results recently obtained during the construction and investigation of these networks. Emphasis is placed on studies producing large-scale interaction data by high-throughput experimental techniques.
Collapse
Affiliation(s)
| | - Kutlu Ö. Ülgen
- Department of Chemical Engineering, Boǧaziçi University, Istanbul, Turkey
| |
Collapse
|
40
|
Diversity in genetic in vivo methods for protein-protein interaction studies: from the yeast two-hybrid system to the mammalian split-luciferase system. Microbiol Mol Biol Rev 2012; 76:331-82. [PMID: 22688816 DOI: 10.1128/mmbr.05021-11] [Citation(s) in RCA: 134] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The yeast two-hybrid system pioneered the field of in vivo protein-protein interaction methods and undisputedly gave rise to a palette of ingenious techniques that are constantly pushing further the limits of the original method. Sensitivity and selectivity have improved because of various technical tricks and experimental designs. Here we present an exhaustive overview of the genetic approaches available to study in vivo binary protein interactions, based on two-hybrid and protein fragment complementation assays. These methods have been engineered and employed successfully in microorganisms such as Saccharomyces cerevisiae and Escherichia coli, but also in higher eukaryotes. From single binary pairwise interactions to whole-genome interactome mapping, the self-reassembly concept has been employed widely. Innovative studies report the use of proteins such as ubiquitin, dihydrofolate reductase, and adenylate cyclase as reconstituted reporters. Protein fragment complementation assays have extended the possibilities in protein-protein interaction studies, with technologies that enable spatial and temporal analyses of protein complexes. In addition, one-hybrid and three-hybrid systems have broadened the types of interactions that can be studied and the findings that can be obtained. Applications of these technologies are discussed, together with the advantages and limitations of the available assays.
Collapse
|
41
|
Physical interaction between coat morphogenetic proteins SpoVID and CotE is necessary for spore encasement in Bacillus subtilis. J Bacteriol 2012; 194:4941-50. [PMID: 22773792 DOI: 10.1128/jb.00914-12] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Endospore formation by Bacillus subtilis is a complex and dynamic process. One of the major challenges of sporulation is the assembly of a protective, multilayered, proteinaceous spore coat, composed of at least 70 different proteins. Spore coat formation can be divided into two distinct stages. The first is the recruitment of proteins to the spore surface, dependent on the morphogenetic protein SpoIVA. The second step, known as encasement, involves the migration of the coat proteins around the circumference of the spore in successive waves, a process dependent on the morphogenetic protein SpoVID and the transcriptional regulation of individual coat genes. We provide genetic and biochemical evidence supporting the hypothesis that SpoVID promotes encasement of the spore by establishing direct protein-protein interactions with other coat morphogenetic proteins. It was previously demonstrated that SpoVID directly interacts with SpoIVA and the inner coat morphogenetic protein, SafA. Here, we show by yeast two-hybrid and pulldown assays that SpoVID also interacts directly with the outer coat morphogenetic protein, CotE. Furthermore, by mutational analysis, we identified a specific residue in the N-terminal domain of SpoVID that is essential for the interaction with CotE but dispensable for the interaction with SafA. We propose an updated model of coat assembly and spore encasement that incorporates several physical interactions between the principal coat morphogenetic proteins.
Collapse
|
42
|
Mäder U, Schmeisky AG, Flórez LA, Stülke J. SubtiWiki--a comprehensive community resource for the model organism Bacillus subtilis. Nucleic Acids Res 2011; 40:D1278-87. [PMID: 22096228 PMCID: PMC3245094 DOI: 10.1093/nar/gkr923] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In the post-genomic era, most components of a cell are known and they can be quantified by large-scale functional genomics approaches. However, genome annotation is the bottleneck that hampers our understanding of living cells and organisms. Up-to-date functional annotation is of special importance for model organisms that provide a frame of reference for studies with other relevant organisms. We have generated a Wiki-type database for the Gram-positive model bacterium Bacillus subtilis, SubtiWiki (http://subtiwiki.uni-goettingen.de/). This Wiki is centered around the individual genes and gene products of B. subtilis and provides information on each aspect of gene function and expression as well as protein activity and its control. SubtiWiki is accompanied by two companion databases SubtiPathways and SubtInteract that provide graphical representations of B. subtilis metabolism and its regulation and of protein-protein interactions, respectively. The diagrams of both databases are easily navigatable using the popular Google maps API, and they are extensively linked with the SubtiWiki gene pages. Moreover, each gene/gene product was assigned to one or more functional categories and transcription factor regulons. Pages for the specific categories and regulons provide a rapid overview of functionally related genes/proteins. Today, SubtiWiki can be regarded as one of the most complete inventories of knowledge on a living organism in one single resource.
Collapse
Affiliation(s)
- Ulrike Mäder
- Interfaculty Institute for Genetics and Functional Genomics, Ernst-Moritz-Arndt-University Greifswald, Jahnstr 15, D-17487 Greifswald, Germany
| | | | | | | |
Collapse
|