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1. E. coli allantoinase is activated by the downstream metabolic enzyme, glycerate kinase, and stabilizes the putative allantoin transporter by direct binding

Author

Rodionova, Irina A, Hosseinnia, Ali, Kim, Sunyoung, Goodacre, Norman, Zhang, Li, Zhang, Zhongge, Palsson, Bernhard, Uetz, Peter, Babu, Mohan, and Saier, Milton H

Subjects
Biochemistry and Cell Biology, Biological Sciences, Allantoin, Escherichia coli, Amidohydrolases, Glyoxylates
Abstract

Allantoin is a good source of ammonium for many organisms, and in Escherichia coli it is utilized under anaerobic conditions. We provide evidence that allantoinase (AllB) is allosterically activated by direct binding of the allantoin catabolic enzyme, glycerate 2-kinase (GlxK) in the presence of glyoxylate. Glyoxylate is known to be an effector of the AllR repressor which regulates the allantoin utilization operons in E. coli. AllB has low affinity for allantoin, but its activation by GlxK leads to increased affinity for its substrate. We also show that the predicted allantoin transporter YbbW (re-named AllW) has allantoin specificity and the protein-protein interaction with AllB. Our results show that the AllB-dependent allantoin degradative pathway is subject to previously unrecognized regulatory mechanisms involving direct protein-protein interactions.

Published
2023

2. A roadmap for the functional annotation of protein families: a community perspective

Author

de Crécy-lagard, Valérie, de Hegedus, Rocio Amorin, Arighi, Cecilia, Babor, Jill, Bateman, Alex, Blaby, Ian, Blaby-Haas, Crysten, Bridge, Alan J, Burley, Stephen K, Cleveland, Stacey, Colwell, Lucy J, Conesa, Ana, Dallago, Christian, Danchin, Antoine, de Waard, Anita, Deutschbauer, Adam, Dias, Raquel, Ding, Yousong, Fang, Gang, Friedberg, Iddo, Gerlt, John, Goldford, Joshua, Gorelik, Mark, Gyori, Benjamin M, Henry, Christopher, Hutinet, Geoffrey, Jaroch, Marshall, Karp, Peter D, Kondratova, Liudmyla, Lu, Zhiyong, Marchler-Bauer, Aron, Martin, Maria-Jesus, McWhite, Claire, Moghe, Gaurav D, Monaghan, Paul, Morgat, Anne, Mungall, Christopher J, Natale, Darren A, Nelson, William C, O’Donoghue, Seán, Orengo, Christine, O’Toole, Katherine H, Radivojac, Predrag, Reed, Colbie, Roberts, Richard J, Rodionov, Dmitri, Rodionova, Irina A, Rudolf, Jeffrey D, Saleh, Lana, Sheynkman, Gloria, Thibaud-Nissen, Francoise, Thomas, Paul D, Uetz, Peter, Vallenet, David, Carter, Erica Watson, Weigele, Peter R, Wood, Valerie, Wood-Charlson, Elisha M, and Xu, Jin

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Human Genome, Genetics, Generic health relevance, Base Sequence, Computational Biology, Genome, Genomics, Molecular Sequence Annotation, Proteins, Data Format, Library and Information Studies, Bioinformatics and computational biology, Data management and data science
Abstract

Over the last 25 years, biology has entered the genomic era and is becoming a science of 'big data'. Most interpretations of genomic analyses rely on accurate functional annotations of the proteins encoded by more than 500 000 genomes sequenced to date. By different estimates, only half the predicted sequenced proteins carry an accurate functional annotation, and this percentage varies drastically between different organismal lineages. Such a large gap in knowledge hampers all aspects of biological enterprise and, thereby, is standing in the way of genomic biology reaching its full potential. A brainstorming meeting to address this issue funded by the National Science Foundation was held during 3-4 February 2022. Bringing together data scientists, biocurators, computational biologists and experimentalists within the same venue allowed for a comprehensive assessment of the current state of functional annotations of protein families. Further, major issues that were obstructing the field were identified and discussed, which ultimately allowed for the proposal of solutions on how to move forward.

Published
2022

4. Protein-Protein-Wechselwirkungen

Author

Uetz, Peter, Ehmoser, Eva-Kathrin, Klostermeier, Dagmar, Richter, Klaus, Curth, Ute, Kurreck, Jens, editor, Engels, Joachim W., editor, and Lottspeich, Friedrich, editor

Published
2022
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5. The protein interactome of Escherichia coli carbohydrate metabolism.

Author

Chowdhury, Shomeek, Fong, Stephen S., and Uetz, Peter

Subjects
CARBOHYDRATE metabolism, ESCHERICHIA coli, PROTEIN-protein interactions, CARBOHYDRATES, ENZYMES
Abstract

We investigate how protein-protein interactions (PPIs) can regulate carbohydrate metabolism in Escherichia coli. We specifically investigated the stoichiometry of 378 PPIs involving carbohydrate metabolic enzymes. In 48 interactions, the interactors were much more abundant than the enzyme and are thus likely to affect enzyme activity and carbohydrate metabolism. Many of these PPIs are conserved across thousands of bacteria including pathogens and microbial species. E. coli adapts to different cellular environments by adjusting the quantities of the interacting proteins (25 PPIs) in a way that the protein-enzyme interaction (PEI) is a likely mechanism to regulate its metabolism in specific environments. We predict 3 PPIs (RpsB-AdhE, DcyD-NanE and MinE-Yccx) previously not known to regulate metabolism. [ABSTRACT FROM AUTHOR]

Published
2025
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6. A Reference Database of Reptile Images.

Author

Uetz, Peter H., Patel, Maya, Gbadamosi, Zainab, Nguyen, Angel, and Shoope, Stacey

Subjects
*DNA data banks, *SCIENCE databases, *DATABASES, *CITIZEN science, *IMAGE databases
Abstract

While there are millions of reptile images available online, they are not well organized and not easily findable, accessible, interoperable, or reproducible (FAIR). More importantly, they are not standardized and thus hardly comparable. Here we present a reference database of more than 14,000 standardized images of 1045 reptile species (969 lizard and 76 snake species) that are based on preserved specimens in 20 different collections, including 533 type species of genera and type specimens of 72 species. All images were taken with standardized views, including dorsal and ventral body shots as well as dorsal, ventral, and lateral views of the heads and other body parts. Although only 11 out of the 20 collections are cross-referenced in VertNet, some others are indexed in GBIF, and this fraction will certainly grow in the near future. The utility of this and similar image collections will further grow with additional material and further cross-referencing, e.g., to DNA sequence databases or citizen science projects. The images are searchable and freely available on Morphobank (Project 5121) and on Figshare. [ABSTRACT FROM AUTHOR]

Published
2024
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7. The uridylyltransferase GlnD and tRNA modification GTPase MnmE allosterically control Escherichia coli folylpoly-γ-glutamate synthase FolC

Author

Rodionova, Irina A, Goodacre, Norman, Do, Jimmy, Hosseinnia, Ali, Babu, Mohan, Uetz, Peter, and Saier, Milton H

Subjects
Biochemistry and Cell Biology, Biological Sciences, Industrial Biotechnology, Prevention, Infectious Diseases, Nutrition, Infection, Allosteric Regulation, Binding Sites, Enzyme Assays, Escherichia coli, Escherichia coli Proteins, Folic Acid, GTP Phosphohydrolases, Gene Expression Regulation, Bacterial, Glutamic Acid, Guanosine Triphosphate, Kinetics, Molecular Docking Simulation, Multienzyme Complexes, Nucleotidyltransferases, Peptide Synthases, Protein Binding, Protein Conformation, alpha-Helical, Protein Conformation, beta-Strand, Protein Interaction Domains and Motifs, Pteroylpolyglutamic Acids, RNA, Transfer, Substrate Specificity, Thermodynamics, Uridine Diphosphate Glucose Dehydrogenase, folate, enzyme kinetics, GTPase, gram-negative bacteria, metabolism, allosteric regulation, cytoplasmic GTP, FolC, G-protein MnmE, tetrahydrofolate polyglutamylation, GlnD, Ugd, MnmE, folate metabolism, amino acid sensing, Chemical Sciences, Medical and Health Sciences, Biochemistry & Molecular Biology, Biological sciences, Biomedical and clinical sciences, Chemical sciences
Abstract

Folate derivatives are important cofactors for enzymes in several metabolic processes. Folate-related inhibition and resistance mechanisms in bacteria are potential targets for antimicrobial therapies and therefore a significant focus of current research. Here, we report that the activity of Escherichia coli poly-γ-glutamyl tetrahydrofolate/dihydrofolate synthase (FolC) is regulated by glutamate/glutamine-sensing uridylyltransferase (GlnD), THF-dependent tRNA modification enzyme (MnmE), and UDP-glucose dehydrogenase (Ugd) as shown by direct in vitro protein-protein interactions. Using kinetics analyses, we observed that GlnD, Ugd, and MnmE activate FolC many-fold by decreasing the K half of FolC for its substrate l-glutamate. Moreover, FolC inhibited the GTPase activity of MnmE at low GTP concentrations. The growth phenotypes associated with these proteins are discussed. These results, obtained using direct in vitro enzyme assays, reveal unanticipated networks of allosteric regulatory interactions in the folate pathway in E. coli and indicate regulation of polyglutamylated tetrahydrofolate biosynthesis by the availability of nitrogen sources, signaled by the glutamine-sensing GlnD protein.

Published
2018

8. The Nitrogen Regulatory PII Protein (GlnB) and N-Acetylglucosamine 6-Phosphate Epimerase (NanE) Allosterically Activate Glucosamine 6-Phosphate Deaminase (NagB) in Escherichia coli.

Author

Rodionova, Irina A, Goodacre, Norman, Babu, Mohan, Emili, Andrew, Uetz, Peter, and Saier, Milton H

Subjects
Escherichia coli, Nitrogen, N-Acetylneuraminic Acid, Aldose-Ketose Isomerases, Racemases and Epimerases, Hexosamines, Glucosamine, Acetylglucosamine, Glucose-6-Phosphate, Escherichia coli Proteins, Transcription Factors, Protein Interaction Mapping, Signal Transduction, Gene Expression Regulation, Bacterial, Phosphorylation, PII Nitrogen Regulatory Proteins, N-acetylglucosamine 6-phosphate epimerase, NagB, NanE, PII, allosteric regulation, glucosamine 6-phosphate deaminase/isomerase, nitrogen regulator, protein-protein interactions, signal transduction, Aetiology, 2.2 Factors relating to the physical environment, Infection, Biological Sciences, Agricultural and Veterinary Sciences, Medical and Health Sciences, Microbiology
Abstract

Amino sugars are good sources of both ammonia and fructose-6-phosphate, produced by the glucosamine 6-phosphate deaminase, NagB. NagB is known to be allosterically regulated by N-acetylglucosamine 6-phosphate (GlcNAc-6P) and the phosphocarrier protein of the bacterial phosphotransferase system, HPr, in Escherichia coli We provide evidence that NanE, GlcNAc-6P epimerase, and the uridylylated PII protein (U-PII) also allosterically activate NagB by direct protein-protein interactions. NanE is essential for neuraminic acid (NANA) and N-acetylmannosamine (ManNAc) utilization, and PII is known to be a central metabolic nitrogen regulator. We demonstrate that uridylylated PII (but not underivatized PII) activates NagB >10-fold at low concentrations of substrate, whereas NanE increases NagB activity >2-fold. NanE activates NagB in the absence or presence of GlcNAc-6P, but HPr and U-PII activation requires the presence of GlcNAc-6P. Activation of NagB by HPr and uridylylated PII, as well as by NanE and HPr (but not by NanE and U-PII), is synergistic, and the modeling, which suggests specific residues involved in complex formation, provides possible explanations. Specific physiological functions for the regulation of NagB by its three protein activators are proposed. Each regulatory agent is suggested to mediate signal transduction in response to a different stimulus.IMPORTANCE The regulation of amino sugar utilization is important for the survival of bacteria in a competitive environment. NagB, a glucosamine 6-phosphate deaminase in Escherichia coli, is essential for amino sugar utilization and is known to be allosterically regulated by N-acetylglucosamine 6-phosphate (GlcNAc-6P) and the histidine-phosphorylatable phosphocarrier protein, HPr. We provide evidence here that NanE, GlcNAc-6P epimerase, and the uridylylated PII protein allosterically activate NagB by direct protein-protein interactions. NanE is essential for N-acetylneuraminic acid (NANA) and N-acetylmannosamine (ManNAc) utilization, and the PII protein is known to be a central metabolic nitrogen regulator. Regulatory links between carbon and nitrogen metabolism are important for adaptation of metabolism to different growth conditions.

Published
2018

9. Global landscape of cell envelope protein complexes in Escherichia coli

Author

Babu, Mohan, Bundalovic-Torma, Cedoljub, Calmettes, Charles, Phanse, Sadhna, Zhang, Qingzhou, Jiang, Yue, Minic, Zoran, Kim, Sunyoung, Mehla, Jitender, Gagarinova, Alla, Rodionova, Irina, Kumar, Ashwani, Guo, Hongbo, Kagan, Olga, Pogoutse, Oxana, Aoki, Hiroyuki, Deineko, Viktor, Caufield, J Harry, Holtzapple, Erik, Zhang, Zhongge, Vastermark, Ake, Pandya, Yogee, Lai, Christine Chieh-lin, El Bakkouri, Majida, Hooda, Yogesh, Shah, Megha, Burnside, Dan, Hooshyar, Mohsen, Vlasblom, James, Rajagopala, Sessandra V, Golshani, Ashkan, Wuchty, Stefan, F Greenblatt, Jack, Saier, Milton, Uetz, Peter, F Moraes, Trevor, Parkinson, John, and Emili, Andrew

Subjects
Medical Microbiology, Biomedical and Clinical Sciences, Biological Sciences, Infection, Generic health relevance, Cell Membrane, Escherichia coli, Membrane Proteins, Multiprotein Complexes, Proteomics
Abstract

Bacterial cell envelope protein (CEP) complexes mediate a range of processes, including membrane assembly, antibiotic resistance and metabolic coordination. However, only limited characterization of relevant macromolecules has been reported to date. Here we present a proteomic survey of 1,347 CEPs encompassing 90% inner- and outer-membrane and periplasmic proteins of Escherichia coli. After extraction with non-denaturing detergents, we affinity-purified 785 endogenously tagged CEPs and identified stably associated polypeptides by precision mass spectrometry. The resulting high-quality physical interaction network, comprising 77% of targeted CEPs, revealed many previously uncharacterized heteromeric complexes. We found that the secretion of autotransporters requires translocation and the assembly module TamB to nucleate proper folding from periplasm to cell surface through a cooperative mechanism involving the β-barrel assembly machinery. We also establish that an ABC transporter of unknown function, YadH, together with the Mla system preserves outer membrane lipid asymmetry. This E. coli CEP 'interactome' provides insights into the functional landscape governing CE systems essential to bacterial growth, metabolism and drug resistance.

Published
2018

10. Citizen science and online data: Opportunities and challenges for snake ecology and action against snakebite

Author

Durso, Andrew M., Ruiz de Castañeda, Rafael, Montalcini, Camille, Mondardini, M. Rosa, Fernandez-Marques, Jose L., Grey, François, Müller, Martin M., Uetz, Peter, Marshall, Benjamin M., Gray, Russell J., Smith, Christopher E., Becker, Donald, Pingleton, Michael, Louies, Jose, Abegg, Arthur D., Akuboy, Jeannot, Alcoba, Gabriel, Daltry, Jennifer C., Entiauspe-Neto, Omar M., Freed, Paul, de Freitas, Marco Antonio, Glaudas, Xavier, Huang, Song, Huang, Tianqi, Kalki, Yatin, Kojima, Yosuke, Laudisoit, Anne, Limbu, Kul Prasad, Martínez-Fonseca, José G., Mebert, Konrad, Rödel, Mark-Oliver, Ruane, Sara, Ruedi, Manuel, Schmitz, Andreas, Tatum, Sarah A., Tillack, Frank, Visvanathan, Avinash, Wüster, Wolfgang, and Bolon, Isabelle

Published
2021
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11. The phosphocarrier protein HPr of the bacterial phosphotransferase system globally regulates energy metabolism by directly interacting with multiple enzymes in Escherichia coli.

Author

Rodionova, Irina A, Zhang, Zhongge, Mehla, Jitender, Goodacre, Norman, Babu, Mohan, Emili, Andrew, Uetz, Peter, and Saier, Milton H

Subjects
Escherichia coli, Phosphoenolpyruvate Sugar Phosphotransferase System, Phosphofructokinase-2, Isoenzymes, Aldose-Ketose Isomerases, Pyruvate Kinase, Adenylate Kinase, Histidine, Bacterial Proteins, Escherichia coli Proteins, Recombinant Proteins, Recombinant Fusion Proteins, Proteomics, Protein Processing, Post-Translational, Allosteric Regulation, Binding Sites, Enzyme Activation, Protein Conformation, Energy Metabolism, Glycolysis, Phosphorylation, Models, Molecular, Protein Interaction Domains and Motifs, Histidine phosphocarrier protein, adenylate kinase, glucosamine 6-phosphate deaminase/isomerase, glycolysis, phosphofructokinase, protein-protein interaction, pyruvate kinase, Affordable and Clean Energy, glucosamine 6-phosphate deaminase, isomerase, Chemical Sciences, Biological Sciences, Medical and Health Sciences, Biochemistry & Molecular Biology
Abstract

The histidine-phosphorylatable phosphocarrier protein (HPr) is an essential component of the sugar-transporting phosphotransferase system (PTS) in many bacteria. Recent interactome findings suggested that HPr interacts with several carbohydrate-metabolizing enzymes, but whether HPr plays a regulatory role was unclear. Here, we provide evidence that HPr interacts with a large number of proteins in Escherichia coli We demonstrate HPr-dependent allosteric regulation of the activities of pyruvate kinase (PykF, but not PykA), phosphofructokinase (PfkB, but not PfkA), glucosamine-6-phosphate deaminase (NagB), and adenylate kinase (Adk). HPr is either phosphorylated on a histidyl residue (HPr-P) or non-phosphorylated (HPr). PykF is activated only by non-phosphorylated HPr, which decreases the PykF Khalf for phosphoenolpyruvate by 10-fold (from 3.5 to 0.36 mm), thus influencing glycolysis. PfkB activation by HPr, but not by HPr-P, resulted from a decrease in the Khalf for fructose-6-P, which likely influences both gluconeogenesis and glycolysis. Moreover, NagB activation by HPr was important for the utilization of amino sugars, and allosteric inhibition of Adk activity by HPr-P, but not by HPr, allows HPr to regulate the cellular energy charge coordinately with glycolysis. These observations suggest that HPr serves as a directly interacting global regulator of carbon and energy metabolism and probably of other physiological processes in enteric bacteria.

Published
2017

12. Conservation status of the world's skinks (Scincidae): Taxonomic and geographic patterns in extinction risk

Author

Chapple, David G., Roll, Uri, Böhm, Monika, Aguilar, Rocío, Amey, Andrew P., Austin, Chris C., Baling, Marleen, Barley, Anthony J., Bates, Michael F., Bauer, Aaron M., Blackburn, Daniel G., Bowles, Phil, Brown, Rafe M., Chandramouli, S.R., Chirio, Laurent, Cogger, Hal, Colli, Guarino R., Conradie, Werner, Couper, Patrick J., Cowan, Mark A., Craig, Michael D., Das, Indraneil, Datta-Roy, Aniruddha, Dickman, Chris R., Ellis, Ryan J., Fenner, Aaron L., Ford, Stewart, Ganesh, S.R., Gardner, Michael G., Geissler, Peter, Gillespie, Graeme R., Glaw, Frank, Greenlees, Matthew J., Griffith, Oliver W., Grismer, L. Lee, Haines, Margaret L., Harris, D. James, Hedges, S. Blair, Hitchmough, Rod A., Hoskin, Conrad J., Hutchinson, Mark N., Ineich, Ivan, Janssen, Jordi, Johnston, Gregory R., Karin, Benjamin R., Keogh, J. Scott, Kraus, Fred, LeBreton, Matthew, Lymberakis, Petros, Masroor, Rafaqat, McDonald, Peter J., Mecke, Sven, Melville, Jane, Melzer, Sabine, Michael, Damian R., Miralles, Aurélien, Mitchell, Nicola J., Nelson, Nicola J., Nguyen, Truong Q., de Campos Nogueira, Cristiano, Ota, Hidetoshi, Pafilis, Panayiotis, Pauwels, Olivier S.G., Perera, Ana, Pincheira-Donoso, Daniel, Reed, Robert N., Ribeiro-Júnior, Marco A., Riley, Julia L., Rocha, Sara, Rutherford, Pamela L., Sadlier, Ross A., Shacham, Boaz, Shea, Glenn M., Shine, Richard, Slavenko, Alex, Stow, Adam, Sumner, Joanna, Tallowin, Oliver J.S., Teale, Roy, Torres-Carvajal, Omar, Trape, Jean-Francois, Uetz, Peter, Ukuwela, Kanishka D.B., Valentine, Leonie, Van Dyke, James U., van Winkel, Dylan, Vasconcelos, Raquel, Vences, Miguel, Wagner, Philipp, Wapstra, Erik, While, Geoffrey M., Whiting, Martin J., Whittington, Camilla M., Wilson, Steve, Ziegler, Thomas, Tingley, Reid, and Meiri, Shai

Published
2021
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17. The global biogeography of lizard functional groups

Author

Vidan, Enav, Novosolov, Maria, Bauer, Aaron M., Herrera, Fernando Castro, Chirio, Laurent, de Campos Nogueira, Cristiano, Doan, Tiffany M., Lewin, Amir, Meirte, Danny, Nagy, Zoltan T., Pincheira-Donoso, Daniel, Tallowin, Oliver J.S., Carvajal, Omar Torres, Uetz, Peter, Wagner, Philipp, Wang, Yuezhao, Belmaker, Jonathan, and Meiri, Shai

Published
2019

21. Extinct, obscure or imaginary: The lizard species with the smallest ranges

Author

Meiri, Shai, Bauer, Aaron M., Allison, Allen, Castro-Herrera, Fernando, Chirio, Laurent, Colli, Guarino, Das, Indraneil, Doan, Tiffany M., Glaw, Frank, Grismer, Lee L., Hoogmoed, Marinus, Kraus, Fred, LeBreton, Matthew, Meirte, Danny, Nagy, Zoltán T., de C. Nogueira, Cristiano, Oliver, Paul, Pauwels, Olivier S. G., Pincheira-Donoso, Daniel, Shea, Glenn, Sindaco, Roberto, Tallowin, Oliver J. S., Torres-Carvajal, Omar, Trape, Jean-Francois, Uetz, Peter, Wagner, Philipp, Wang, Yuezhao, Ziegler, Thomas, and Roll, Uri

Published
2018

22. Evolutionarily conserved herpesviral protein interaction networks.

Author

Fossum, Even, Friedel, Caroline C, Rajagopala, Seesandra V, Titz, Björn, Baiker, Armin, Schmidt, Tina, Kraus, Theo, Stellberger, Thorsten, Rutenberg, Christiane, Suthram, Silpa, Bandyopadhyay, Sourav, Rose, Dietlind, von Brunn, Albrecht, Uhlmann, Mareike, Zeretzke, Christine, Dong, Yu-An, Boulet, Hélène, Koegl, Manfred, Bailer, Susanne M, Koszinowski, Ulrich, Ideker, Trey, Uetz, Peter, Zimmer, Ralf, and Haas, Jürgen

Subjects
Hela Cells, Humans, Herpesviridae, Herpesvirus 1, Human, Herpesvirus 3, Human, Muromegalovirus, Herpesvirus 4, Human, Herpesvirus 8, Human, Virion, Viral Proteins, Viral Core Proteins, Immunohistochemistry, Cluster Analysis, Protein Interaction Mapping, Evolution, Molecular, Phylogeny, Signal Transduction, HeLa Cells, Evolution, Molecular, Herpesvirus 1, Human, Herpesvirus 3, Herpesvirus 4, Herpesvirus 8, Virology, Microbiology, Immunology, Medical Microbiology
Abstract

Herpesviruses constitute a family of large DNA viruses widely spread in vertebrates and causing a variety of different diseases. They possess dsDNA genomes ranging from 120 to 240 kbp encoding between 70 to 170 open reading frames. We previously reported the protein interaction networks of two herpesviruses, varicella-zoster virus (VZV) and Kaposi's sarcoma-associated herpesvirus (KSHV). In this study, we systematically tested three additional herpesvirus species, herpes simplex virus 1 (HSV-1), murine cytomegalovirus and Epstein-Barr virus, for protein interactions in order to be able to perform a comparative analysis of all three herpesvirus subfamilies. We identified 735 interactions by genome-wide yeast-two-hybrid screens (Y2H), and, together with the interactomes of VZV and KSHV, included a total of 1,007 intraviral protein interactions in the analysis. Whereas a large number of interactions have not been reported previously, we were able to identify a core set of highly conserved protein interactions, like the interaction between HSV-1 UL33 with the nuclear egress proteins UL31/UL34. Interactions were conserved between orthologous proteins despite generally low sequence similarity, suggesting that function may be more conserved than sequence. By combining interactomes of different species we were able to systematically address the low coverage of the Y2H system and to extract biologically relevant interactions which were not evident from single species.

Published
2009

24. The protein network of bacterial motility

Author

Rajagopala, Seesandra V, Titz, Bjorn, Goll, Johannes, Parrish, Jodi R, Wohlbold, Katrin, McKevitt, Matthew T, Palzkill, Timothy, Mori, Hirotada, Finley, Russell L, Uetz, Peter, Rajagopala, Seesandra V, Titz, Bjorn, Goll, Johannes, Parrish, Jodi R, Wohlbold, Katrin, McKevitt, Matthew T, Palzkill, Timothy, Mori, Hirotada, Finley, Russell L, and Uetz, Peter

Abstract

Motility is achieved in most bacterial species by the flagellar apparatus. It consists of dozens of different proteins with thousands of individual subunits. The published literature about bacterial chemotaxis and flagella documented 51 protein?protein interactions (PPIs) so far. We have screened whole genome two‐hybrid arrays of Treponema pallidum and Campylobacter jejuni for PPIs involving known flagellar proteins and recovered 176 and 140 high‐confidence interactions involving 110 and 133 proteins, respectively. To explore the biological relevance of these interactions, we tested an Escherichia coli gene deletion array for motility defects (using swarming assays) and found 159 gene deletion strains to have reduced or no motility. Comparing our interaction data with motility phenotypes from E. coli, Bacillus subtilis, and Helicobacter pylori, we found 23 hitherto uncharacterized proteins involved in motility. Integration of phylogenetic information with our interaction and phenotyping data reveals a conserved core of motility proteins, which appear to have recruited many additional species‐specific components over time. Our interaction data also predict 18 110 interactions for 64 flagellated bacteria.Mol Syst Biol. 3: 128

Published
2023

25. The Escherichia coli K-12 ORFeome: a resource for comparative molecular microbiology

Author

Rajagopala, Seesandra V., Yamamoto, Natsuko, Zweifel, Adrienne E., Nakamichi, Tomoko, Huang, Hsi-Kuang, Mendez-Rios, Jorge David, Franca-Koh, Jonathan, Boorgula, Meher Preethi, Fujita, Kazutoshi, Suzuki, Ken-ichirou, Hu, James C., Wanner, Barry L., Mori, Hirotada, Uetz, Peter, Rajagopala, Seesandra V., Yamamoto, Natsuko, Zweifel, Adrienne E., Nakamichi, Tomoko, Huang, Hsi-Kuang, Mendez-Rios, Jorge David, Franca-Koh, Jonathan, Boorgula, Meher Preethi, Fujita, Kazutoshi, Suzuki, Ken-ichirou, Hu, James C., Wanner, Barry L., Mori, Hirotada, and Uetz, Peter

Abstract

We have constructed an open reading frame (ORFeome) collection of 3974 or 94% of the known Escherichia coli K-12 ORFs in Gateway® entry vector pENTR/Zeo. The collection has been used for protein expression and protein interaction studies. For example, we have compared interactions among YgjD, YjeE and YeaZ proteins in E. coli, Streptococcus pneumoniae, and Staphylococcus aureus. We also compare this ORFeome with other Gateway-compatible bacterial ORFeomes and show its utility for comparative functional genomics., Background, Systems biology and functional genomics require genome-wide datasets and resources. Complete sets of cloned open reading frames (ORFs) have been made for about a dozen bacterial species and allow researchers to express and study complete proteomes in a high-throughput fashion., Results, Conclusions, The E. coli ORFeome provides a useful resource for functional genomics and other areas of protein research in a highly flexible format. Our comparison with other ORFeomes makes comparative analyses straighforward and facilitates direct comparisons of many proteins across many genomes.

Published
2023

26. E. coli allantoinase is activated by the downstream metabolic enzyme, glycerate kinase, and stabilizes the putative allantoin transporter by direct binding

Author

Rodionova, Irina A., Hosseinnia, Ali, Kim, Sunyoung, Goodacre, Norman, Zhang, Li, Zhang, Zhongge, Palsson, Bernhard, Uetz, Peter, Babu, Mohan, Saier, Milton H., Babu , Mohan, Rodionova, Irina A., Hosseinnia, Ali, Kim, Sunyoung, Goodacre, Norman, Zhang, Li, Zhang, Zhongge, Palsson, Bernhard, Uetz, Peter, Babu, Mohan, Saier, Milton H., and Babu , Mohan

Abstract

Allantoin is a good source of ammonium for many organisms, and in Escherichia coli it is utilized under anaerobic conditions. We provide evidence that allantoinase (AllB) is allosterically activated by direct binding of the allantoin catabolic enzyme, glycerate 2-kinase (GlxK) in the presence of glyoxylate. Glyoxylate is known to be an effector of the AllR repressor which regulates the allantoin utilization operons in E. coli. AllB has low affinity for allantoin, but its activation by GlxK leads to increased affinity for its substrate. We also show that the predicted allantoin transporter YbbW (re-named AllW) has allantoin specificity and the protein–protein interaction with AllB. Our results show that the AllB-dependent allantoin degradative pathway is subject to previously unrecognized regulatory mechanisms involving direct protein–protein interactions.

Published
2023

28. The global distribution of tetrapods reveals a need for targeted reptile conservation

Author

Roll, Uri, Feldman, Anat, Novosolov, Maria, Allison, Allen, Bauer, Aaron M., Bernard, Rodolphe, Böhm, Monika, Castro-Herrera, Fernando, Chirio, Laurent, Collen, Ben, Colli, Guarino R., Dabool, Lital, Das, Indraneil, Doan, Tiffany M., Grismer, Lee L., Hoogmoed, Marinus, Itescu, Yuval, Kraus, Fred, LeBreton, Matthew, Lewin, Amir, Martins, Marcio, Maza, Erez, Meirte, Danny, Nagy, Zoltán T., de C. Nogueira, Cristiano, Pauwels, Olivier S. G., Pincheira-Donoso, Daniel, Powney, Gary D., Sindaco, Roberto, Tallowin, Oliver J. S., Torres-Carvajal, Omar, Trape, Jean-François, Vidan, Enav, Uetz, Peter, Wagner, Philipp, Wang, Yuezhao, Orme, C. David L., Grenyer, Richard, and Meiri, Shai

Published
2017
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38. A Globally Integrated Structure of Taxonomy supporting biodiversity science and conservation

Author

Sandall, Emily, primary, Maureaud, Aurore, additional, Guralnick, Robert, additional, McGeoch, Melodie, additional, Sica, Yanina, additional, Rogan, Matthew, additional, Booher, Douglas, additional, Costello, Mark, additional, Edwards, Robert, additional, Franz, Nico, additional, Ingenloff, Kate, additional, Lucas, Maisha, additional, Marsh, Charles, additional, McGowan, Jennifer, additional, Pinkert, Stefan, additional, Ranipeta, Ajay, additional, Uetz, Peter, additional, Wieczorek, John, additional, and Jetz, Walter, additional

Published
2022
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39. A global analysis of viviparity in squamates highlights its prevalence in cold climates

Author

Zimin, Anna, primary, Zimin, Sean V., additional, Shine, Richard, additional, Avila, Luciano, additional, Bauer, Aaron, additional, Böhm, Monika, additional, Brown, Rafe, additional, Barki, Goni, additional, de Oliveira Caetano, Gabriel Henrique, additional, Castro Herrera, Fernando, additional, Chapple, David G., additional, Chirio, Laurent, additional, Colli, Guarino R., additional, Doan, Tiffany M., additional, Glaw, Frank, additional, Grismer, L. Lee, additional, Itescu, Yuval, additional, Kraus, Fred, additional, LeBreton, Matthew, additional, Martins, Marcio, additional, Morando, Mariana, additional, Murali, Gopal, additional, Nagy, Zoltán T., additional, Novosolov, Maria, additional, Oliver, Paul, additional, Passos, Paulo, additional, Pauwels, Olivier S. G., additional, Pincheira‐Donoso, Daniel, additional, Ribeiro‐Junior, Marco Antonio, additional, Shea, Glenn, additional, Tingley, Reid, additional, Torres‐Carvajal, Omar, additional, Trape, Jean‐François, additional, Uetz, Peter, additional, Wagner, Philipp, additional, Roll, Uri, additional, and Meiri, Shai, additional

Published
2022
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40. Getting the GIST: Testing an integrative data structure for linking taxonomy, biodiversity and conservation

Author

Sandall, Emily, primary, Maureaud, Aurore, additional, Guralnick, Robert, additional, McGeoch, Melodie, additional, Sica, Yanina, additional, Rogan, Matthew, additional, Booher, Doug, additional, Costello, Mark, additional, Edwards, Robert, additional, Franz, Nico, additional, Ingenloff, Kate, additional, Lucas, Maisha, additional, Marsh, Charles, additional, McGowan, Jennifer, additional, Pinkert, Stefan, additional, Ranipeta, Ajay, additional, Uetz, Peter, additional, Wieczorek, John, additional, and Jetz, Walter, additional

Published
2022
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42. The Burmese python genome reveals the molecular basis for extreme adaptation in snakes

Author

Castoe, Todd A., de Koning, A. P. Jason, Hall, Kathryn T., Card, Daren C., Schield, Drew R., Fujita, Matthew K., Ruggiero, Robert P., Degner, Jack F., Daza, Juan M., Gu, Wanjun, Reyes-Velasco, Jacobo, Shaney, Kyle J., Castoe, Jill M., Fox, Samuel E., Poole, Alex W., Polanco, Daniel, Dobry, Jason, Vandewege, Michael W., Li, Qing, Schott, Ryan K., Kapusta, Aurélie, Minx, Patrick, Feschotte, Cédric, Uetz, Peter, Ray, David A., Hoffmann, Federico G., Bogden, Robert, Smith, Eric N., Chang, Belinda S. W., Vonk, Freek J., Casewell, Nicholas R., Henkel, Christiaan V., Richardson, Michael K., Mackessy, Stephen P., Bronikowsi, Anne M., Yandell, Mark, Warren, Wesley C., Secor, Stephen M., and Pollock, David D.

Published
2013

44. The Magnitude of Global Marine Species Diversity

Author

Appeltans, Ward, Ahyong, Shane T., Anderson, Gary, Angel, Martin V., Artois, Tom, Bailly, Nicolas, Bamber, Roger, Barber, Anthony, Bartsch, Ilse, Berta, Annalisa, Błażewicz-Paszkowycz, Magdalena, Bock, Phil, Boxshall, Geoff, Boyko, Christopher B., Brandão, Simone Nunes, Bray, Rod A., Bruce, Niel L., Cairns, Stephen D., Chan, Tin-Yam, Cheng, Lanna, Collins, Allen G., Cribb, Thomas, Curini-Galletti, Marco, Dahdouh-Guebas, Farid, Davie, Peter J.F., Dawson, Michael N., De Clerck, Olivier, Decock, Wim, De Grave, Sammy, de Voogd, Nicole J., Domning, Daryl P., Emig, Christian C., Erséus, Christer, Eschmeyer, William, Fauchald, Kristian, Fautin, Daphne G., Feist, Stephen W., Fransen, Charles H.J.M., Furuya, Hidetaka, Garcia-Alvarez, Oscar, Gerken, Sarah, Gibson, David, Gittenberger, Arjan, Gofas, Serge, Gómez-Daglio, Liza, Gordon, Dennis P., Guiry, Michael D., Hernandez, Francisco, Hoeksema, Bert W., Hopcroft, Russell R., Jaume, Damià, Kirk, Paul, Koedam, Nico, Koenemann, Stefan, Kolb, Jürgen B., Kristensen, Reinhardt M., Kroh, Andreas, Lambert, Gretchen, Lazarus, David B., Lemaitre, Rafael, Longshaw, Matt, Lowry, Jim, Macpherson, Enrique, Madin, Laurence P., Mah, Christopher, Mapstone, Gill, McLaughlin, Patsy A., Mees, Jan, Meland, Kenneth, Messing, Charles G., Mills, Claudia E., Molodtsova, Tina N., Mooi, Rich, Neuhaus, Birger, Ng, Peter K.L., Nielsen, Claus, Norenburg, Jon, Opresko, Dennis M., Osawa, Masayuki, Paulay, Gustav, Perrin, William, Pilger, John F., Poore, Gary C.B., Pugh, Phil, Read, Geoffrey B., Reimer, James D., Rius, Marc, Rocha, Rosana M., Saiz-Salinas, José I., Scarabino, Victor, Schierwater, Bernd, Schmidt-Rhaesa, Andreas, Schnabel, Kareen E., Schotte, Marilyn, Schuchert, Peter, Schwabe, Enrico, Segers, Hendrik, Self-Sullivan, Caryn, Shenkar, Noa, Siegel, Volker, Sterrer, Wolfgang, Stöhr, Sabine, Swalla, Billie, Tasker, Mark L., Thuesen, Erik V., Timm, Tarmo, Todaro, M. Antonio, Turon, Xavier, Tyler, Seth, Uetz, Peter, van der Land, Jacob, Vanhoorne, Bart, van Ofwegen, Leen P., van Soest, Rob W.M., Vanaverbeke, Jan, Walker-Smith, Genefor, Walter, T. Chad, Warren, Alan, Williams, Gary C., Wilson, Simon P., and Costello, Mark J.

Published
2012
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48. A global analysis of viviparity in squamates highlights its prevalence in cold climates

Author

Zimin, Anna, Zimin, Sean V., Shine, Richard, Avila, Luciano, Bauer, Aaron, Böhm, Monika, Brown, Rafe, Barki, Goni, de Oliveira Caetano, Gabriel Henrique, Castro Herrera, Fernando, Chapple, David G., Chirio, Laurent, Colli, Guarino R., Doan, Tiffany M., Glaw, Frank, Grismer, L. Lee, Itescu, Yuval, Kraus, Fred, LeBreton, Matthew, Martins, Marcio, Morando, Mariana, Murali, Gopal, Nagy, Zoltán T., Novosolov, Maria, Oliver, Paul, Passos, Paulo, Pauwels, Olivier S. G., Pincheira-Donoso, Daniel, Ribeiro-Junior, Marco Antonio, Shea, Glenn, Tingley, Reid, Torres-Carvajal, Omar, Trape, Jean-François, Uetz, Peter, Wagner, Philipp, Roll, Uri, Meiri, Shai, Zimin, Anna, Zimin, Sean V., Shine, Richard, Avila, Luciano, Bauer, Aaron, Böhm, Monika, Brown, Rafe, Barki, Goni, de Oliveira Caetano, Gabriel Henrique, Castro Herrera, Fernando, Chapple, David G., Chirio, Laurent, Colli, Guarino R., Doan, Tiffany M., Glaw, Frank, Grismer, L. Lee, Itescu, Yuval, Kraus, Fred, LeBreton, Matthew, Martins, Marcio, Morando, Mariana, Murali, Gopal, Nagy, Zoltán T., Novosolov, Maria, Oliver, Paul, Passos, Paulo, Pauwels, Olivier S. G., Pincheira-Donoso, Daniel, Ribeiro-Junior, Marco Antonio, Shea, Glenn, Tingley, Reid, Torres-Carvajal, Omar, Trape, Jean-François, Uetz, Peter, Wagner, Philipp, Roll, Uri, and Meiri, Shai

Abstract

Aim: Viviparity has evolved more times in squamates than in any other vertebrate group; therefore, squamates offer an excellent model system in which to study the patterns, drivers and implications of reproductive mode evolution. Based on current species distributions, we examined three selective forces hypothesized to drive the evolution of squamate viviparity (cold climate, variable climate and hypoxic conditions) and tested whether viviparity is associated with larger body size. Location: Global. Time period: Present day. Taxon: Squamata. Methods: We compiled a dataset of 9061 squamate species, including their distributions, elevation, climate, body mass and reproductive modes. We applied species-level and assemblage-level approaches for predicting reproductive mode, both globally and within biogeographical realms. We tested the relationships of temperature, interannual and intra-annual climatic variation, elevation (as a proxy for hypoxic conditions) and body mass with reproductive mode, using path analyses to account for correlations among the environmental predictors. Results: Viviparity was strongly associated with cold climates at both species and assemblage levels, despite the prevalence of viviparity in some warm climates. Viviparity was not clearly correlated with climatic variability or elevation. The probability of being viviparous exhibited a weak positive correlation with body size. Conclusions: Although phylogenetic history is important, potentially explaining the occurrence of viviparous species in regions that are warm at present, current global squamate distribution is characterized by a higher relative abundance of viviparity in cold environments, supporting the prediction of the “cold-climate” hypothesis. The roles of climatic variation and hypoxia are less important and not straightforward. Elevation probably exerts various selective pressures and influences the prevalence of viviparity primarily through its effect on temperature rather than

Published
2022

49. Project data and code access underlying the globally integrated taxonomic structure

Author

McGeoch, Melodie A., McGowan, Jennifer, Edwards, Robert, Maisha Lucas, Ranipeta, Ajay, Uetz, Peter, Jetz, Walter, Sandall, Emily L., Sica, Yanina V., Rogan, Matthew S., Pinkert, Stefan, Marsh, Charles J., Wieczorek, John, Ingenloff, Kate, Maureaud, Aurore, Franz, Nico, Guralnick, Robert, and Booher, Douglas B.

Abstract

Data and code underlying the project and manuscript on an integrated structure of taxonomy

Published
2022
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50. The binary protein-protein interaction landscape of Escherichia coli

Author

Rajagopala, Seesandra V, Sikorski, Patricia, Kumar, Ashwani, Mosca, Roberto, Vlasblom, James, Arnold, Roland, Franca-Koh, Jonathan, Pakala, Suman B, Phanse, Sadhna, Ceol, Arnaud, Häuser, Roman, Siszler, Gabriella, Wuchty, Stefan, Emili, Andrew, Babu, Mohan, Aloy, Patrick, Pieper, Rembert, and Uetz, Peter

Published
2014
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