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2. What Makes a Bacterial Species Pathogenic?:Comparative Genomic Analysis of the Genus Leptospira.

Author

Fouts, Derrick E, Matthias, Michael A, Adhikarla, Haritha, Adler, Ben, Amorim-Santos, Luciane, Berg, Douglas E, Bulach, Dieter, Buschiazzo, Alejandro, Chang, Yung-Fu, Galloway, Renee L, Haake, David A, Haft, Daniel H, Hartskeerl, Rudy, Ko, Albert I, Levett, Paul N, Matsunaga, James, Mechaly, Ariel E, Monk, Jonathan M, Nascimento, Ana LT, Nelson, Karen E, Palsson, Bernhard, Peacock, Sharon J, Picardeau, Mathieu, Ricaldi, Jessica N, Thaipandungpanit, Janjira, Wunder, Elsio A, Yang, X Frank, Zhang, Jun-Jie, and Vinetz, Joseph M

Subjects
Animals, Humans, Leptospira, Leptospirosis, Protein Sorting Signals, Bacterial Proteins, Genomics, Evolution, Molecular, Phylogeny, Virulence, Base Sequence, Genome, Bacterial, Molecular Sequence Data, Bacterial Secretion Systems, Evolution, Molecular, Genome, Bacterial, Biological Sciences, Medical and Health Sciences, Tropical Medicine
Abstract

Leptospirosis, caused by spirochetes of the genus Leptospira, is a globally widespread, neglected and emerging zoonotic disease. While whole genome analysis of individual pathogenic, intermediately pathogenic and saprophytic Leptospira species has been reported, comprehensive cross-species genomic comparison of all known species of infectious and non-infectious Leptospira, with the goal of identifying genes related to pathogenesis and mammalian host adaptation, remains a key gap in the field. Infectious Leptospira, comprised of pathogenic and intermediately pathogenic Leptospira, evolutionarily diverged from non-infectious, saprophytic Leptospira, as demonstrated by the following computational biology analyses: 1) the definitive taxonomy and evolutionary relatedness among all known Leptospira species; 2) genomically-predicted metabolic reconstructions that indicate novel adaptation of infectious Leptospira to mammals, including sialic acid biosynthesis, pathogen-specific porphyrin metabolism and the first-time demonstration of cobalamin (B12) autotrophy as a bacterial virulence factor; 3) CRISPR/Cas systems demonstrated only to be present in pathogenic Leptospira, suggesting a potential mechanism for this clade's refractoriness to gene targeting; 4) finding Leptospira pathogen-specific specialized protein secretion systems; 5) novel virulence-related genes/gene families such as the Virulence Modifying (VM) (PF07598 paralogs) proteins and pathogen-specific adhesins; 6) discovery of novel, pathogen-specific protein modification and secretion mechanisms including unique lipoprotein signal peptide motifs, Sec-independent twin arginine protein secretion motifs, and the absence of certain canonical signal recognition particle proteins from all Leptospira; and 7) and demonstration of infectious Leptospira-specific signal-responsive gene expression, motility and chemotaxis systems. By identifying large scale changes in infectious (pathogenic and intermediately pathogenic) vs. non-infectious Leptospira, this work provides new insights into the evolution of a genus of bacterial pathogens. This work will be a comprehensive roadmap for understanding leptospirosis pathogenesis. More generally, it provides new insights into mechanisms by which bacterial pathogens adapt to mammalian hosts.

Published
2016

3. Evolutionary classification of CRISPR–Cas systems: a burst of class 2 and derived variants

Author

Makarova, Kira S., Wolf, Yuri I., Iranzo, Jaime, Shmakov, Sergey A., Alkhnbashi, Omer S., Brouns, Stan J. J., Charpentier, Emmanuelle, Cheng, David, Haft, Daniel H., Horvath, Philippe, Moineau, Sylvain, Mojica, Francisco J. M., Scott, David, Shah, Shiraz A., Siksnys, Virginijus, Terns, Michael P., Venclovas, Česlovas, White, Malcolm F., Yakunin, Alexander F., Yan, Winston, Zhang, Feng, Garrett, Roger A., Backofen, Rolf, van der Oost, John, Barrangou, Rodolphe, and Koonin, Eugene V.

Published
2020
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4. Creating a specialist protein resource network: a meeting report for the protein bioinformatics and community resources retreat

Author

Babbitt, Patricia C, Bagos, Pantelis G, Bairoch, Amos, Bateman, Alex, Chatonnet, Arnaud, Chen, Mark Jinan, Craik, David J, Finn, Robert D, Gloriam, David, Haft, Daniel H, Henrissat, Bernard, Holliday, Gemma L, Isberg, Vignir, Kaas, Quentin, Landsman, David, Lenfant, Nicolas, Manning, Gerard, Nagano, Nozomi, Srinivasan, Narayanaswamy, O’Donovan, Claire, Pruitt, Kim D, Sowdhamini, Ramanathan, Rawlings, Neil D, Saier, Milton H, Sharman, Joanna L, Spedding, Michael, Tsirigos, Konstantinos D, Vastermark, Ake, and Vriend, Gerrit

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, 2.6 Resources and infrastructure (aetiology), 1.5 Resources and infrastructure (underpinning), Aetiology, Underpinning research, Generic health relevance, Computational Biology, Congresses as Topic, Databases, Nucleic Acid, Databases, Protein, Humans, Molecular Sequence Annotation, Proteins, Data Format, Library and Information Studies, Bioinformatics and computational biology, Data management and data science
Abstract

During 11-12 August 2014, a Protein Bioinformatics and Community Resources Retreat was held at the Wellcome Trust Genome Campus in Hinxton, UK. This meeting brought together the principal investigators of several specialized protein resources (such as CAZy, TCDB and MEROPS) as well as those from protein databases from the large Bioinformatics centres (including UniProt and RefSeq). The retreat was divided into five sessions: (1) key challenges, (2) the databases represented, (3) best practices for maintenance and curation, (4) information flow to and from large data centers and (5) communication and funding. An important outcome of this meeting was the creation of a Specialist Protein Resource Network that we believe will improve coordination of the activities of its member resources. We invite further protein database resources to join the network and continue the dialogue.

Published
2015

7. Genome Analysis of Multiple Pathogenic Isolates of Streptococcus agalactiae: Implications for the Microbial "Pan-Genome"

Author

Tettelin, Hervé, Masignani, Vega, Cieslewicz, Michael J., Donati, Claudio, Medini, Duccio, Ward, Naomi L., Angiuoli, Samuel V., Crabtree, Jonathan, Jones, Amanda L., Durkin, A. Scott, DeBoy, Robert T., Davidsen, Tanja M., Mora, Marirosa, Scarselli, Maria, Peterson, Jeremy D., Hauser, Christopher R., Sundaram, Jaideep P., Nelson, William C., Madupu, Ramana, Brinkac, Lauren M., Dodson, Robert J., Rosovitz, Mary J., Sullivan, Steven A., Daugherty, Sean C., Haft, Daniel H., Selengut, Jeremy, Gwinn, Michelle L., Zhou, Liwei, Zafar, Nikhat, Khouri, Hoda, Radune, Diana, Dimitrov, George, Watkins, Kisha, Smith, Shannon, Utterback, Teresa R., White, Owen, Rubens, Craig E., Grandi, Guido, Madoff, Lawrence C., Kasper, Dennis L., Telford, John L., Wessels, Michael R., Rappuoli, Rino, and Fraser, Claire M.

Published
2005

8. Structural Flexibility in the Burkholderia mallei Genome

Author

Nierman, William C., DeShazer, David, Kim, H. Stanley, Tettelin, Herve, Nelson, Karen E., Feldblyum, Tamara, Ulrich, Ricky L., Ronning, Catherine M., Brinkac, Lauren M., Daugherty, Sean C., Davidsen, Tanja D., Deboy, Robert T., Dimitrov, George, Dodson, Robert J., Durkin, A. Scott, Gwinn, Michelle L., Haft, Daniel H., Khouri, Hoda, Kolonay, James F., Madupu, Ramana, Mohammoud, Yasmin, Nelson, William C., Radune, Diana, Romero, Claudia M., Sarria, Saul, Selengut, Jeremy, Shamblin, Christine, Sullivan, Steven A., White, Owen, Yu, Yan, Zafar, Nikhat, Zhou, Liwei, Fraser, Claire M., and Greenberg, E. Peter

Published
2004

9. The Complete Genome Sequence of the Arabidopsis and Tomato Pathogen Pseudomonas syringae pv. tomato DC3000

Author

Buell, C. Robin, Joardar, Vinita, Lindeberg, Magdalen, Selengut, Jeremy, Paulsen, Ian T., Gwinn, Michelle L., Dodson, Robert J., Deboy, Robert T., Durkin, A. Scott, Kolonay, James F., Madupu, Ramana, Daugherty, Sean, Brinkac, Lauren, Beanan, Maureen J., Haft, Daniel H., Nelson, William C., Davidsen, Tanja, Zafar, Nikhat, Zhou, Liwei, Liu, Jia, Yuan, Qiaoping, Khouri, Hoda, Fedorova, Nadia, Tran, Bao, Russell, Daniel, Berry, Kristi, Utterback, Teresa, Van Aken, Susan E., Feldblyum, Tamara V., D'Ascenzo, Mark, Deng, Wen-Ling, Ramos, Adela R., Alfano, James R., Cartinhour, Samuel, Chatterjee, Arun K., Delaney, Terrence P., Lazarowitz, Sondra G., Martin, Gregory B., Schneider, David J., Tang, Xiaoyan, Bender, Carol L., White, Owen, Fraser, Claire M., and Collmer, Alan

Published
2003

10. The Complete Genome Sequence of Chlorobium tepidum TLS, A Photosynthetic, Anaerobic, Green-Sulfur Bacterium

Author

Eisen, Jonathan A., Nelson, Karen E., Paulsen, Ian T., Heidelberg, John F., Wu, Martin, Dodson, Robert J., Deboy, Robert, Gwinn, Michelle L., Nelson, William C., Haft, Daniel H., Hickey, Erin K., Peterson, Jeremy D., Durkin, A. Scott, Kolonay, James L., Yang, Fan, Holt, Ingeborg, Umayam, Lowell A., Mason, Tanya, Brenner, Michael, Shea, Terrance P., Parksey, Debbie, Nierman, William C., Feldblyum, Tamara V., Hansen, Cheryl L., Craven, M. Brook, Radune, Diana, Vamathevan, Jessica, Khouri, Hoda, White, Owen, Gruber, Tanja M., Ketchum, Karen A., Venter, J. Craig, Tettelin, Hervé, Bryant, Donald A., and Fraser, Claire M.

Published
2002

11. Complete Genome Sequence of a Virulent Isolate of Streptococcus pneumoniae

Author

Tettelin, Hervé, Nelson, Karen E., Paulsen, Ian T., Eisen, Jonathan A., Read, Timothy D., Peterson, Scott, Heidelberg, John, DeBoy, Robert T., Haft, Daniel H., Dodson, Robert J., Durkin, A. Scott, Gwinn, Michelle, Kolonay, James F., Nelson, William C., Peterson, Jeremy D., Umayam, Lowell A., White, Owen, Salzberg, Steven L., Lewis, Matthew R., Radune, Diana, Holtzapple, Erik, Khouri, Hoda, Wolf, Alex M., Utterback, Terry R., Hansen, Cheryl L., McDonald, Lisa A., Feldblyum, Tamara V., Angiuoli, Samuel, Dickinson, Tanja, Hickey, Erin K., Holt, Ingeborg E., Loftus, Brendan J., Yang, Fan, Smith, Hamilton O., Venter, J. Craig, Dougherty, Brian A., Morrison, Donald A., Hollingshead, Susan K., and Fraser, Claire M.

Published
2001

12. Complete Genome Sequence of Caulobacter crescentus

Author

Nierman, William C., Feldblyum, Tamara V., Laub, Michael T., Paulsen, Ian T., Nelson, Karen E., Eisen, Jonathan, Heidelberg, John F., Alley, M. R. K., Ohta, Noriko, Maddock, Janine R., Potocka, Isabel, Nelson, William C., Newton, Austin, Stephens, Craig, Phadke, Nikhil D., Ely, Bert, DeBoy, Robert T., Dodson, Robert J., Durkin, A. Scott, Gwinn, Michelle L., Haft, Daniel H., Kolonay, James F., Smit, John, Craven, M. B., Khouri, Hoda, Shetty, Jyoti, Berry, Kristi, Utterback, Teresa, Tran, Kevin, Wolf, Alex, Vamathevan, Jessica, Ermolaeva, Maria, White, Owen, Salzberg, Steven L., Venter, J. Craig, Shapiro, Lucy, and Fraser, Claire M.

Published
2001

14. Comparative Genomics of Emerging Human Ehrlichiosis Agents

Author

Hotopp, Julie C Dunning, Lin, Mingqun, Madupu, Ramana, Crabtree, Jonathan, Angiuoli, Samuel V, Eisen, Jonathan, Seshadri, Rekha, Ren, Qinghu, Wu, Martin, Utterback, Teresa R, Smith, Shannon, Lewis, Matthew, Khouri, Hoda, Zhang, Chunbin, Niu, Hua, Lin, Quan, Ohashi, Norio, Zhi, Ning, Nelson, William, Brinkac, Lauren M, Dodson, Robert J, Rosovitz, MJ, Sundaram, Jaideep, Daugherty, Sean C, Davidsen, Tanja, Durkin, Anthony S, Gwinn, Michelle, Haft, Daniel H, Selengut, Jeremy D, Sullivan, Steven A, Zafar, Nikhat, Zhou, Liwei, Benahmed, Faiza, Forberger, Heather, Halpin, Rebecca, Mulligan, Stephanie, Robinson, Jeffrey, White, Owen, Rikihisa, Yasuko, and Tettelin, Hervé

Subjects
Infectious Diseases, Rare Diseases, Genetics, Biotechnology, Vector-Borne Diseases, Prevention, Emerging Infectious Diseases, Infection, Good Health and Well Being, Animals, Biotin, DNA Repair, Ehrlichia, Ehrlichiosis, Genome, Genomics, Humans, Models, Biological, Phylogeny, Rickettsia, Ticks, Developmental Biology
Abstract

Anaplasma (formerly Ehrlichia) phagocytophilum, Ehrlichia chaffeensis, and Neorickettsia (formerly Ehrlichia) sennetsu are intracellular vector-borne pathogens that cause human ehrlichiosis, an emerging infectious disease. We present the complete genome sequences of these organisms along with comparisons to other organisms in the Rickettsiales order. Ehrlichia spp. and Anaplasma spp. display a unique large expansion of immunodominant outer membrane proteins facilitating antigenic variation. All Rickettsiales have a diminished ability to synthesize amino acids compared to their closest free-living relatives. Unlike members of the Rickettsiaceae family, these pathogenic Anaplasmataceae are capable of making all major vitamins, cofactors, and nucleotides, which could confer a beneficial role in the invertebrate vector or the vertebrate host. Further analysis identified proteins potentially involved in vacuole confinement of the Anaplasmataceae, a life cycle involving a hematophagous vector, vertebrate pathogenesis, human pathogenesis, and lack of transovarial transmission. These discoveries provide significant insights into the biology of these obligate intracellular pathogens. © 2006 Dunning Hotopp.

Published
2006

15. Complete Genome Sequence of Neisseria meningitidis Serogroup B Strain MC58

Author

Tettelin, Hervé, Saunders, Nigel J., Heidelberg, John, Jeffries, Alex C., Nelson, Karen E., Eisen, Jonathan A., Ketchum, Karen A., Hood, Derek W., Peden, John F., Dodson, Robert J., Nelson, William C., Gwinn, Michelle L., DeBoy, Robert, Peterson, Jeremy D., Hickey, Erin K., Haft, Daniel H., Salzberg, Steven L., White, Owen, Fleischmann, Robert D., Dougherty, Brian A., Mason, Tanya, Ciecko, Anne, Parksey, Debbie S., Blair, Eric, Cittone, Henry, Clark, Emily B., Cotton, Matthew D., Utterback, Terry R., Khouri, Hoda, Qin, Haiying, Vamathevan, Jessica, Gill, John, Scarlato, Vincenzo, Masignani, Vega, Pizza, Mariagrazia, Grandi, Guido, Sun, Li, Smith, Hamilton O., Fraser, Claire M., Moxon, E. Richard, Rappuoli, Rino, and Venter, J. Craig

Published
2000

16. Life in hot carbon monoxide: the complete genome sequence of Carboxydothermus hydrogenoformans Z-2901.

Author

Wu, Martin, Ren, Qinghu, Durkin, A Scott, Daugherty, Sean C, Brinkac, Lauren M, Dodson, Robert J, Madupu, Ramana, Sullivan, Steven A, Kolonay, James F, Haft, Daniel H, Nelson, William C, Tallon, Luke J, Jones, Kristine M, Ulrich, Luke E, Gonzalez, Juan M, Zhulin, Igor B, Robb, Frank T, and Eisen, Jonathan A

Subjects
Peptococcaceae, Carbon Monoxide, Sequence Analysis, DNA, Genomics, Base Sequence, Oxidative Stress, Genes, Bacterial, Genome, Bacterial, Models, Biological, Molecular Sequence Data, Hot Temperature, Genes, Bacterial, Genome, Models, Biological, Sequence Analysis, DNA, Genetics, Developmental Biology
Abstract

We report here the sequencing and analysis of the genome of the thermophilic bacterium Carboxydothermus hydrogenoformans Z-2901. This species is a model for studies of hydrogenogens, which are diverse bacteria and archaea that grow anaerobically utilizing carbon monoxide (CO) as their sole carbon source and water as an electron acceptor, producing carbon dioxide and hydrogen as waste products. Organisms that make use of CO do so through carbon monoxide dehydrogenase complexes. Remarkably, analysis of the genome of C. hydrogenoformans reveals the presence of at least five highly differentiated anaerobic carbon monoxide dehydrogenase complexes, which may in part explain how this species is able to grow so much more rapidly on CO than many other species. Analysis of the genome also has provided many general insights into the metabolism of this organism which should make it easier to use it as a source of biologically produced hydrogen gas. One surprising finding is the presence of many genes previously found only in sporulating species in the Firmicutes Phylum. Although this species is also a Firmicutes, it was not known to sporulate previously. Here we show that it does sporulate and because it is missing many of the genes involved in sporulation in other species, this organism may serve as a "minimal" model for sporulation studies. In addition, using phylogenetic profile analysis, we have identified many uncharacterized gene families found in all known sporulating Firmicutes, but not in any non-sporulating bacteria, including a sigma factor not known to be involved in sporulation previously.

Published
2005

17. Genome Sequence of the Radioresistant Bacterium Deinococcus radiodurans R1

Author

White, Owen, Eisen, Jonathan A., Heidelberg, John F., Hickey, Erin K., Peterson, Jeremy D., Dodson, Robert J., Haft, Daniel H., Gwinn, Michelle L., Nelson, William C., Richardson, Delwood L., Moffat, Kelly S., Qin, Haiying, Jiang, Lingxia, Pamphile, Wanda, Crosby, Marie, Shen, Mian, Vamathevan, Jessica J., Lam, Peter, McDonald, Lisa, Utterback, Terry, Zalewski, Celeste, Makarova, Kira S., Aravind, L., Daly, Michael J., Minton, Kenneth W., Fleischmann, Robert D., Ketchum, Karen A., Nelson, Karen E., Salzberg, Steven, Smith, Hamilton O., Venter, J. Craig, and Fraser, Claire M.

Published
1999

23. InterPro in 2022

Author

Paysan-Lafosse, Typhaine, primary, Blum, Matthias, additional, Chuguransky, Sara, additional, Grego, Tiago, additional, Pinto, Beatriz Lázaro, additional, Salazar, Gustavo A, additional, Bileschi, Maxwell L, additional, Bork, Peer, additional, Bridge, Alan, additional, Colwell, Lucy, additional, Gough, Julian, additional, Haft, Daniel H, additional, Letunić, Ivica, additional, Marchler-Bauer, Aron, additional, Mi, Huaiyu, additional, Natale, Darren A, additional, Orengo, Christine A, additional, Pandurangan, Arun P, additional, Rivoire, Catherine, additional, Sigrist, Christian J A, additional, Sillitoe, Ian, additional, Thanki, Narmada, additional, Thomas, Paul D, additional, Tosatto, Silvio C E, additional, Wu, Cathy H, additional, and Bateman, Alex, additional

Published
2022
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27. Consensus on β-Lactamase Nomenclature

Author

Bradford, Patricia A., primary, Bonomo, Robert A., additional, Bush, Karen, additional, Carattoli, Alessandra, additional, Feldgarden, Michael, additional, Haft, Daniel H., additional, Ishii, Yoshikazu, additional, Jacoby, George A., additional, Klimke, William, additional, Palzkill, Timothy, additional, Poirel, Laurent, additional, Rossolini, Gian Maria, additional, Tamma, Pranita D., additional, and Arias, Cesar A., additional

Published
2022
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29. InterPro in 2022.

Author

Paysan-Lafosse, Typhaine, Blum, Matthias, Chuguransky, Sara, Grego, Tiago, Pinto, Beatriz Lázaro, Salazar, Gustavo A, Bileschi, Maxwell L, Bork, Peer, Bridge, Alan, Colwell, Lucy, Gough, Julian, Haft, Daniel H, Letunić, Ivica, Marchler-Bauer, Aron, Mi, Huaiyu, Natale, Darren A, Orengo, Christine A, Pandurangan, Arun P, Rivoire, Catherine, and Sigrist, Christian J A

Published
2023
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31. A standard numbering scheme for class c β-lactamases

Author

Mack, Andrew R., Barnes, Melissa D., Taracila, Magdalena A., Hujer, Andrea M., Hujer, Kristine M., Cabot, Gabriel, Feldgarden, Michael, Haft, Daniel H., Klimke, William, Akker, Focco van den, Vila, Alejandro J., Smania, Andrea, Haider, Shozeb, Papp-Wallace, Krisztina M., Bradford, Patricia A., Rossolini, Gian Maria, Docquier, Jean-Denis, Frère, Jean-Marie, Galleni, Moreno, Hanson, Nancy D., Oliver, Antonio, Plésiatyz, Patrick, Poirel, Laurent, Nordmann, Patrice, Palzkill, Timothy G., Jacoby, George A., Bush, Karen, and Bonomo, Robert A.

Abstract

Unlike for classes A and B, a standardized amino acid numbering scheme has not been proposed for the class C (AmpC) β-lactamases, which complicates communication in the field. Here, we propose a scheme developed through a collaborative approach that considers both sequence and structure, preserves traditional numbering of catalytically important residues (Ser64, Lys67, Tyr150, and Lys315), is adaptable to new variants or enzymes yet to be discovered and includes a variation for genetic and epidemiological applications.

Published
2021

32. Unexpected abundance of coenzyme F420-dependent enzymes in Mycobacterium tuberculosis and other actinobacteria

Author

Selengut, Jeremy D. and Haft, Daniel H.

Subjects
Coenzymes -- Physiological aspects, Coenzymes -- Genetic aspects, Mycobacterium tuberculosis -- Physiological aspects, Mycobacterium tuberculosis -- Genetic aspects, Tuberculosis -- Development and progression, Biological sciences
Abstract

Regimens targeting Mycobacterium tuberculosis, the causative agent of tuberculosis (TB), require long courses of treatment and a combination of three or more drugs. An increase in drug-resistant strains of M. tuberculosis demonstrates the need for additional TB-specific drugs. A notable feature of M. tuberculosis is coenzyme [F.sub.420], which is distributed sporadically and sparsely among prokaryotes. This distribution allows for comparative genomics-based investigations. Phylogenetic profiling (comparison of differential gene content) based on [F.sub.420] biosynthesis nominated many actinobacterial proteins as candidate [F.sub.420]-dependent enzymes. Three such families dominated the results: the luciferase-like monooxygenase (LLM), pyridoxamine 5'-phosphate oxidase (PPOX), and deazaflavin-dependent nitroreductase (DDN) families. The DDN family was determined to be limited to [F.sub.420]-producing species. The LLM and PPOX families were observed in [F.sub.420]-producing species as well as species lacking [F.sub.420] but were particularly numerous in many actinobacterial species, including M. tuberculosis. Partitioning the LLM and PPOX families based on an organism's ability to make [F.sub.420] allowed the application of the SIMBAL (sites inferred by metabolic background assertion labeling) profiling method to identify [F.sub.420]-correlated subsequences. These regions were found to correspond to flavonoid cofactor binding sites. Significantly, these results showed that M. tuberculosis carries at least 28 separate [F.sub.420]-dependent enzymes, most of unknown function, and a paucity of flavin mononucleotide (FMN)-dependent proteins in these families. While prevalent in mycobacteria, markers of [F.sub.420] biosynthesis appeared to be absent from the normal human gut flora. These findings suggest that M. tuberculosis relies heavily on coenzyme [F.sub.420] for its redox reactions. This dependence and the cofactor's rarity may make [F.sub.420]-related proteins promising drug targets. doi: 10.1128/JB.00425-10

Published
2010

35. Evolutionary classification of CRISPR-Cas systems:a burst of class 2 and derived variants

Author

Makarova, Kira S., Wolf, Yuri I., Iranzo, Jaime, Shmakov, Sergey A., Alkhnbashi, Omer S., Brouns, Stan J. J., Charpentier, Emmanuelle, Cheng, David, Haft, Daniel H., Horvath, Philippe, Moineau, Sylvain, Mojica, Francisco J. M., Scott, David, Shah, Shiraz A., Siksnys, Virginijus, Terns, Michael P., Venclovas, Česlovas, White, Malcolm F., Yakunin, Alexander F., Yan, Winston, Zhang, Feng, Garrett, Roger Antony, Backofen, Rolf, van der Oost, John, Barrangou, Rodolphe, Koonin, Eugene V., Makarova, Kira S., Wolf, Yuri I., Iranzo, Jaime, Shmakov, Sergey A., Alkhnbashi, Omer S., Brouns, Stan J. J., Charpentier, Emmanuelle, Cheng, David, Haft, Daniel H., Horvath, Philippe, Moineau, Sylvain, Mojica, Francisco J. M., Scott, David, Shah, Shiraz A., Siksnys, Virginijus, Terns, Michael P., Venclovas, Česlovas, White, Malcolm F., Yakunin, Alexander F., Yan, Winston, Zhang, Feng, Garrett, Roger Antony, Backofen, Rolf, van der Oost, John, Barrangou, Rodolphe, and Koonin, Eugene V.

Abstract

The number and diversity of known CRISPR-Cas systems have substantially increased in recent years. Here, we provide an updated evolutionary classification of CRISPR-Cas systems and cas genes, with an emphasis on the major developments that have occurred since the publication of the latest classification, in 2015. The new classification includes 2 classes, 6 types and 33 subtypes, compared with 5 types and 16 subtypes in 2015. A key development is the ongoing discovery of multiple, novel class 2 CRISPR-Cas systems, which now include 3 types and 17 subtypes. A second major novelty is the discovery of numerous derived CRISPR-Cas variants, often associated with mobile genetic elements that lack the nucleases required for interference. Some of these variants are involved in RNA-guided transposition, whereas others are predicted to perform functions distinct from adaptive immunity that remain to be characterized experimentally. The third highlight is the discovery of numerous families of ancillary CRISPR-linked genes, often implicated in signal transduction. Together, these findings substantially clarify the functional diversity and evolutionary history of CRISPR-Cas.

Published
2020

36. Evolution and classification of the CRISPR/Cas systems

Author

Makarova, Kira S., Devillers, Rodolphe, Haft, Daniel H., Moineau, Sylvain, Brouns, Stan J. J., Charpentier, Emmanuelle, Horvath, Philippe, Mojica, Francisco Juan Martínez, Wolf, Yuri I., Yakunin, Alexander F., Oost, John van der, Koonin, Eugene V., Makarova, Kira S., Devillers, Rodolphe, Haft, Daniel H., Moineau, Sylvain, Brouns, Stan J. J., Charpentier, Emmanuelle, Horvath, Philippe, Mojica, Francisco Juan Martínez, Wolf, Yuri I., Yakunin, Alexander F., Oost, John van der, and Koonin, Eugene V.

Abstract

The CRISPR–Cas (clustered regularly interspaced short palindromic repeats–CRISPR-associated proteins) modules are adaptive immunity systems that are present in many archaea and bacteria. These defence systems are encoded by operons that have an extraordinarily diverse architecture and a high rate of evolution for both the cas genes and the unique spacer content. Here, we provide an updated analysis of the evolutionary relationships between CRISPR–Cas systems and Cas proteins. Three major types of CRISPR–Cas system are delineated, with a further division into several subtypes and a few chimeric variants. Given the complexity of the genomic architectures and the extremely dynamic evolution of the CRISPR–Cas systems, a unified classification of these systems should be based on multiple criteria. Accordingly, we propose a 'polythetic' classification that integrates the phylogenies of the most common cas genes, the sequence and organization of the CRISPR repeats and the architecture of the CRISPR–cas loci.

Published
2020

37. Comparative genomic evidence for a close relationship between the dimorphic prosthecate bacteria Hyphomonas neptunium and Caulobacter crescentus

Author

Badger, Jonathan H., Hoover, Timothy R., Brun, Yves V., Weiner, Ronald M., Laub, Michael T., Alexandre, Gladys, Mrazek, Jan, Ren, Qinghu, Paulsen, Ian T., Nelson, Karen E., Khouri, Hoda M., Radune, Diana, Sosa, Julia, Dodson, Robert J., Sullivan, Steven A., Rosovitz, M.J., Madupu, Ramana, Brinkac, Lauren M., Durkin, A. Scott, Daugherty, Sean C., Kothari, Sagar P., Giglio, Michelle Gwinn, Zhou, Liwei, Haft, Daniel H., Selengut, Jeremy D., Davidsen, Tanja M., Yang, Qi, Zafar, Nikhat, and Ward, Naomi L.

Subjects
Caulobacter -- Genetic aspects, Chemotaxis -- Research, Biological sciences
Abstract

The dimorphic prosthecate bacteria (DPB) are [alpha]-proteobacteria that reproduce in an asymmetric manner rather than by binary fission and are of interest as simple models of development. Prior to this work, the only member of this group for which genome sequence was available was the model freshwater organism Caulobacter crescentus. Here we describe the genome sequence of Hyphomonas neptunium, a marine member of the DPB that differs from C. crescentus in that H. neptunium uses its stalk as a reproductive structure. Genome analysis indicates that this organism shares more genes with C. crescentus than it does with Silicibacter pomeroyi (a closer relative according to 16S rRNA phylogeny), that it relies upon a heterotrophic strategy utilizing a wide range of substrates, that its cell cycle is likely to be regulated in a similar manner to that of C. crescentus, and that the outer membrane complements of H. neptunium and C. crescentus are remarkably similar. H. neptunium swarmer cells are highly motile via a single polar flagellum. With the exception of cheY and cheR, genes required for chemotaxis were absent in the H. neptunium genome. Consistent with this observation, H. neptunium swarmer cells did not respond to any chemotactic stimuli that were tested, which suggests that H. neptunium motility is a random dispersal mechanism for swarmer cells rather than a stimulus-controlled navigation system for locating specific environments. In addition to providing insights into bacterial development, the H. neptunium genome will provide an important resource for the study of other interesting biological processes including chromosome segregation, polar growth, and cell aging.

Published
2006

38. Insights on evolution Of virulence and resistance from the complete genome analysis of an early methicillin-resistant Staphylococcus aureus strain and a biofilm-producing methicillin-resistant Staphylococcus epidermidis strain

Author

Gill, Steven R., Fouts, Derrick E., Archer, Gordon L., Mongodin, Emmanuel F., DeBoy, Robert T., Ravel, Jacques, Paulsen, Ian T., Kolonay, James F., Brinkac, Lauren, Beanan, Mauren, Dodson, Robert J., Daugherty, Sean C., Madupu, Ramana, Angiuoli, Samuel V., Durkin, A. Scott, Haft, Daniel H., Vamathevan, Jessica, Khouri, Hoda, Utterback, Terry, Lee, Chris, Dimitrov, George, Jiang, Lingxia, Qin, Haiying, Weidman, Jan, Tran, Kevin, Kang, Kathy, Hance, Ioana R., Nelson, Karen E., and Fraser, Claire M.

Subjects
Bacterial genetics -- Research, Bacteriology -- Research, Staphylococcus aureus -- Research, Staphylococcus aureus -- Genetic aspects, Drug resistance in microorganisms -- Research, Drug resistance in microorganisms -- Genetic aspects, Biological sciences
Abstract

Staphylococcus aureus is an opportunistic pathogen and the major causative agent of numerous hospital- and community-acquired infections. Staphylococcus epidermidis has emerged as a causative agent of infections often associated with implanted medical devices. We have sequenced the ~2.8-Mb genome of S. aureus COL, an early methicillin-resistant isolate, and the ~2.6-Mb genome of S. epidermidis RP62a, a methicillin-resistant biofilm isolate. Comparative analysis of these and other staphylococcal genomes was used to explore the evolution of virulence and resistance between these two species. The S. aureus and S. epidermidis genomes are syntenic throughout their lengths and share a core set of 1,681 open reading frames. Genome islands in nonsyntenic regions are the primary source of variations in pathogenicity and resistance. Gene transfer between staphylococci and low-GC-content gram-positive bacteria appears to have shaped their virulence and resistance profiles. Integrated plasmids in S. epidermidis carry genes encoding resistance to cadmium and species-specific LPXTG surface proteins. A novel genome island encodes multiple phenol-soluble modulins, a potential S. epidermidis virulence factor. S. epidermidis contains the cap operon, encoding the polyglutamate capsule, a major virulence factor in Bacillus anthracis. Additional phenotypic differences are likely the result of single nucleotide polymorphisms, which are most numerous in cell envelope proteins. Overall differences in pathogenicity can be attributed to genome islands in S. aureus which encode enterotoxins, exotoxins, leukocidins, and leukotoxins not found in S. epidermidis.

Published
2005

39. Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment

Author

Moran, Mary Ann, Buchan, Alison, Gonzalez, Jose M., Heidelberg, John F., Whitman, William B., Kiene, Ronald P., Henriksen, James R., King, Gary M., Belas, Robert, Fuqua, Clay, Brinkac, Lauren, Lewis, Matt, Johri, Shivani, Weaver, Bruce, Pai, Grace, Eisen, Jonathan A., Rahe, Elisha, Sheldon, Wade M., Ye, Wenying, Miller, Todd R., Carlton, Jane, Rasko, David A., Paulsen, Ian T., Ren, Qinghu, Daugherty, Sean C., Deboy, Robert T., Dodson, Robert J., Durkin, A. Scott, Madupu, Ramana, Nelson, William C., Sullivan, Steven A., Rosovitz, M. J., Haft, Daniel H., Selengut, Jeremy, and Ward, Naomi

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): Mary Ann Moran (corresponding author) [1]; Alison Buchan [3]; José M. González [4]; John F. Heidelberg [5]; William B. Whitman [2]; Ronald P. Kiene [6]; James R. Henriksen [2]; [...]

Published
2004
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42. Complete genome sequence of the oral pathogenic bacterium Porphyromonas gingivalis strain W83

Author

Nelson, Karen E., Fleischmann, Robert D., DeBoy, Robert T., Paulsen, Ian T., Fouts, Derrick E., Eisen, Jonathan A., Daugherty, Sean C., Dodson, Robert J., Durkin, A. Scott, Gwinn, Michelle, Haft, Daniel H., Kolonay, James F., Nelson, William C., Mason, Tanya, Tallon, Luke, Gray, Jessica, Granger, David, Tettelin, Herne, Dong, Hong, Galvin, Jamie L, Duncan, Margaret J., Dewhirst, Floyd E., and Fraser, Claire M.

Subjects
Periodontal disease -- Causes of, Sulfur bacteria -- Physiological aspects, Pathogenic microorganisms -- Genetic aspects, Bacteriology -- Research, Genomes -- Physiological aspects, Biological sciences
Abstract

The complete 2,343,479-bp genome sequence of the gram-negative, pathogenic oral bacterium Porphyromonas gingivalis strain W83, a major contributor to periodontal disease, was determined. Whole-genome comparative analysis with other available complete genome sequences confirms the close relationship between the Cyto-phaga-Flavobacteria-Bacteroides (CFB) phylum and the green-sulfur bacteria. Within the CFB phyla, the genomes most similar to that of P. gingivalis are those of Bacteroides thetaiotaomicron and B. fragilis. Outside of the CFB phyla the most similar genome to P. gingivalis is that of Chlorobium tepidum, supporting the previous phylogenetic studies that indicated that the Chlorobia and CFB phyla are related, albeit distantly. Genome analysis of strain W83 reveals a range of pathways and virulence determinants that relate to the novel biology of this oral pathogen. Among these determinants are at least six putative hemagglutinin-like genes and 36 previously unidentified peptidases. Genome analysis also reveals that P. gingivalis can metabolize a range of amino acids and generate a number of metabolic end products that are toxic to the human host or human gingival tissue and contribute to the development of periodontal disease.

Published
2003

43. The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria

Author

Read, Timothy D., Peterson, Scott N., Tourasse, Nicolas, Baillie, Les W., Paulsen, Ian T., Nelson, Karen E., Tettelin, Herve, Fouts, Derrick E., Eisen, Jonathan A., Gill, Steven R., Holtzapple, Erik K., Okstad, Ole Andreas, Helgason, Erlendur, Rilstone, Jennifer, Wu, Martin, Kolonay, James F., Beanan, Maureen J., Dodson, Robert J., Brinkac, Lauren M., Gwinn, Michelle, DeBoy, Robert T., Madpu, Ramana, Daugherty, Sean C., Durkin, A. Scott, Haft, Daniel H., Nelson, William C., Peterson, Jeremy D., Pop, Mihai, Khouri, Hoda M., Radune, Diana, Benton, Jonathan L., Mahamoud, Yasmin, Jiang, Lingxia, Hance, Ioana R., Weidman, Janice F., Berry, Kristi J., Plaut, Roger D., Wolf, Alex M., Watkins, Kisha L., Nierman, William C., Hazen, Alyson, Cline, Robin, Redmond, Caroline, Thwaite, Joanne E., White, Owen, Salzberg, Steven L., Thomason, Brendan, Friedlander, Arthur M., Koehler, Theresa M., Hanna, Philip C., Kolsto, Anne-Brit, and Fraser, Claire M.

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): Timothy D. Read (corresponding author) [1, 2]; Scott N. Peterson [1, 3]; Nicolas Tourasse [4, 7]; Les W. Baillie [1, 2, 5]; Ian T. Paulsen [1, 6]; Karen E. [...]

Published
2003

44. DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae

Author

Heidelberg, John F., Eisen, Jonathan A., Nelson, William C., Clayton, Rebecca A., Gwinn, Michelle L., Dodson, Robert J., Haft, Daniel H., Hickey, Erin K., Peterson, Jeremy D., Umayam, Lowell, Gill, Steven R., Nelson, Karen E., Read, Timothy D., Tettelin, Hervé, Richardson, Delwood, Ermolaeva, Maria D., Vamathevan, Jessica, Bass, Steven, Qin, Haiying, Dragoi, Ioana, Sellers, Patrick, McDonald, Lisa, Utterback, Teresa, Fleishmann, Robert D., Nierman, William C., White, Owen, Salzberg, Steven L., Smith, Hamilton O., Colwell, Rita R., Mekalanos, John J., Venter, J. Craig, and Fraser, Claire M.

Published
2000
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45. RefSeq: expanding the Prokaryotic Genome Annotation Pipeline reach with protein family model curation

Author

Li, Wenjun, primary, O’Neill, Kathleen R, additional, Haft, Daniel H, additional, DiCuccio, Michael, additional, Chetvernin, Vyacheslav, additional, Badretdin, Azat, additional, Coulouris, George, additional, Chitsaz, Farideh, additional, Derbyshire, Myra K, additional, Durkin, A Scott, additional, Gonzales, Noreen R, additional, Gwadz, Marc, additional, Lanczycki, Christopher J, additional, Song, James S, additional, Thanki, Narmada, additional, Wang, Jiyao, additional, Yamashita, Roxanne A, additional, Yang, Mingzhang, additional, Zheng, Chanjuan, additional, Marchler-Bauer, Aron, additional, and Thibaud-Nissen, Françoise, additional

Published
2020
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46. The InterPro protein families and domains database: 20 years on

Author

Blum, Matthias, primary, Chang, Hsin-Yu, additional, Chuguransky, Sara, additional, Grego, Tiago, additional, Kandasaamy, Swaathi, additional, Mitchell, Alex, additional, Nuka, Gift, additional, Paysan-Lafosse, Typhaine, additional, Qureshi, Matloob, additional, Raj, Shriya, additional, Richardson, Lorna, additional, Salazar, Gustavo A, additional, Williams, Lowri, additional, Bork, Peer, additional, Bridge, Alan, additional, Gough, Julian, additional, Haft, Daniel H, additional, Letunic, Ivica, additional, Marchler-Bauer, Aron, additional, Mi, Huaiyu, additional, Natale, Darren A, additional, Necci, Marco, additional, Orengo, Christine A, additional, Pandurangan, Arun P, additional, Rivoire, Catherine, additional, Sigrist, Christian J A, additional, Sillitoe, Ian, additional, Thanki, Narmada, additional, Thomas, Paul D, additional, Tosatto, Silvio C E, additional, Wu, Cathy H, additional, Bateman, Alex, additional, and Finn, Robert D, additional

Published
2020
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47. Erratum for Feldgarden et al., “Validating the AMRFinder Tool and Resistance Gene Database by Using Antimicrobial Resistance Genotype-Phenotype Correlations in a Collection of Isolates”

Author

Feldgarden, Michael, primary, Brover, Vyacheslav, additional, Haft, Daniel H., additional, Prasad, Arjun B., additional, Slotta, Douglas J., additional, Tolstoy, Igor, additional, Tyson, Gregory H., additional, Zhao, Shaohua, additional, Hsu, Chih-Hao, additional, McDermott, Patrick F., additional, Tadesse, Daniel A., additional, Morales, Cesar, additional, Simmons, Mustafa, additional, Tillman, Glenn, additional, Wasilenko, Jamie, additional, Folster, Jason P., additional, and Klimke, William, additional

Published
2020
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48. A Standard Numbering Scheme for Class C β-Lactamases

Author

Mack, Andrew R., primary, Barnes, Melissa D., additional, Taracila, Magdalena A., additional, Hujer, Andrea M., additional, Hujer, Kristine M., additional, Cabot, Gabriel, additional, Feldgarden, Michael, additional, Haft, Daniel H., additional, Klimke, William, additional, van den Akker, Focco, additional, Vila, Alejandro J., additional, Smania, Andrea, additional, Haider, Shozeb, additional, Papp-Wallace, Krisztina M., additional, Bradford, Patricia A., additional, Rossolini, Gian Maria, additional, Docquier, Jean-Denis, additional, Frère, Jean-Marie, additional, Galleni, Moreno, additional, Hanson, Nancy D., additional, Oliver, Antonio, additional, Plésiat, Patrick, additional, Poirel, Laurent, additional, Nordmann, Patrice, additional, Palzkill, Timothy G., additional, Jacoby, George A., additional, Bush, Karen, additional, and Bonomo, Robert A., additional

Published
2020
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