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Wu Y, Garushyants SK, van den Hurk A, Aparicio-Maldonado C, Kushwaha SK, King CM, Ou Y, Todeschini TC, Clokie MRJ, Millard AD, Gençay YE, Koonin EV, Nobrega FL. Bacterial defense systems exhibit synergistic anti-phage activity. Cell Host Microbe 2024; 32:557-572.e6. [PMID: 38402614 PMCID: PMC11009048 DOI: 10.1016/j.chom.2024.01.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 01/23/2024] [Accepted: 01/30/2024] [Indexed: 02/27/2024]
Abstract
Bacterial defense against phage predation involves diverse defense systems acting individually and concurrently, yet their interactions remain poorly understood. We investigated >100 defense systems in 42,925 bacterial genomes and identified numerous instances of their non-random co-occurrence and negative association. For several pairs of defense systems significantly co-occurring in Escherichia coli strains, we demonstrate synergistic anti-phage activity. Notably, Zorya II synergizes with Druantia III and ietAS defense systems, while tmn exhibits synergy with co-occurring systems Gabija, Septu I, and PrrC. For Gabija, tmn co-opts the sensory switch ATPase domain, enhancing anti-phage activity. Some defense system pairs that are negatively associated in E. coli show synergy and significantly co-occur in other taxa, demonstrating that bacterial immune repertoires are largely shaped by selection for resistance against host-specific phages rather than negative epistasis. Collectively, these findings demonstrate compatibility and synergy between defense systems, allowing bacteria to adopt flexible strategies for phage defense.
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Affiliation(s)
- Yi Wu
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Sofya K Garushyants
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Anne van den Hurk
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | | | - Simran Krishnakant Kushwaha
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK; Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani, Rajasthan, India
| | - Claire M King
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Yaqing Ou
- Wellcome Centre for Cell-Matrix Research, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Thomas C Todeschini
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Martha R J Clokie
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Andrew D Millard
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | | | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Franklin L Nobrega
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK.
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Kushwaha SK, Kumar AA, Gupta H, Marathe SA. The Phylogenetic Study of the CRISPR-Cas System in Enterobacteriaceae. Curr Microbiol 2023; 80:196. [PMID: 37118221 DOI: 10.1007/s00284-023-03298-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 04/07/2023] [Indexed: 04/30/2023]
Abstract
The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-CRISPR-associated (Cas) system is a bacterial and archaeal adaptive immune system undergoing rapid multifaceted evolution. This evolution plausibly occurs due to the genetic exchanges of complete loci or individual entities. Here, we systematically investigate the evolutionary framework of the CRISPR-Cas system in six Enterobacteriaceae species and its evolutionary association with housekeeping genes as determined by the gyrB phenogram. The strains show high variability in the cas3 gene and the CRISPR1 locus among the closely related Enterobacteriaceae species, hinting at a series of genetic exchanges. The CRISPR leader is conserved, especially toward the distal end, and could be a core region of the leader. The spacers are conserved within the strains of most species, while some strains show unique sets of spacers. However, inter-species spacer conservation was rarely observed. For a considerable proportion of these spacers, protospacer sources were not detected. These results advance our understanding of the dynamics of the CRISPR-Cas system; however, the biological functions are yet to be characterised.
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Affiliation(s)
- Simran Krishnakant Kushwaha
- Department of Biological Sciences, Faculty Division-III, Birla Institute of Technology & Science, 3277-B, Pilani Campus, Pilani, Rajasthan, 333031, India
| | - Aryahi A Kumar
- Department of Biological Sciences, Faculty Division-III, Birla Institute of Technology & Science, 3277-B, Pilani Campus, Pilani, Rajasthan, 333031, India
| | - Hardik Gupta
- Department of Biological Sciences, Faculty Division-III, Birla Institute of Technology & Science, 3277-B, Pilani Campus, Pilani, Rajasthan, 333031, India
| | - Sandhya Amol Marathe
- Department of Biological Sciences, Faculty Division-III, Birla Institute of Technology & Science, 3277-B, Pilani Campus, Pilani, Rajasthan, 333031, India.
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Kushwaha SK, Bhavesh NLS, Abdella B, Lahiri C, Marathe SA. The phylogenomics of CRISPR-Cas system and revelation of its features in Salmonella. Sci Rep 2020; 10:21156. [PMID: 33273523 PMCID: PMC7712790 DOI: 10.1038/s41598-020-77890-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 11/18/2020] [Indexed: 01/26/2023] Open
Abstract
Salmonellae display intricate evolutionary patterns comprising over 2500 serovars having diverse pathogenic profiles. The acquisition and/or exchange of various virulence factors influences the evolutionary framework. To gain insights into evolution of Salmonella in association with the CRISPR-Cas genes we performed phylogenetic surveillance across strains of 22 Salmonella serovars. The strains differed in their CRISPR1-leader and cas operon features assorting into two main clades, CRISPR1-STY/cas-STY and CRISPR1-STM/cas-STM, comprising majorly typhoidal and non-typhoidal Salmonella serovars respectively. Serovars of these two clades displayed better relatedness, concerning CRISPR1-leader and cas operon, across genera than between themselves. This signifies the acquisition of CRISPR1/Cas region could be through a horizontal gene transfer event owing to the presence of mobile genetic elements flanking CRISPR1 array. Comparison of CRISPR and cas phenograms with that of multilocus sequence typing (MLST) suggests differential evolution of CRISPR/Cas system. As opposed to broad-host-range, the host-specific serovars harbor fewer spacers. Mapping of protospacer sources suggested a partial correlation of spacer content with habitat diversity of the serovars. Some serovars like serovar Enteritidis and Typhimurium that inhabit similar environment/infect similar hosts hardly shared their protospacer sources.
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Affiliation(s)
- Simran Krishnakant Kushwaha
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani, Rajasthan, India.
| | - Narra Lakshmi Sai Bhavesh
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani, Rajasthan, India
| | - Bahaa Abdella
- Department of Biological Sciences, Sunway University, Petaling Jaya, Selangor, Malaysia.,Faculty of Aquatic and Fisheries Sciences, Kafrelsheikh University, Kafrelsheikh, Egypt
| | - Chandrajit Lahiri
- Department of Biological Sciences, Sunway University, Petaling Jaya, Selangor, Malaysia
| | - Sandhya Amol Marathe
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani, Rajasthan, India.
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Winiarski MJ, Wiendlocha B, Gołąb S, Kushwaha SK, Wiśniewski P, Kaczorowski D, Thompson JD, Cava RJ, Klimczuk T. Superconductivity in CaBi2. Phys Chem Chem Phys 2016; 18:21737-45. [PMID: 27435423 DOI: 10.1039/c6cp02856j] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Superconductivity is observed with critical temperature Tc = 2.0 K in self-flux-grown single crystals of CaBi2. This material adopts the ZrSi2 structure type with lattice parameters a = 4.696(1) Å, b = 17.081(2) Å and c = 4.611(1) Å. The crystals of CaBi2 were studied by means of magnetic susceptibility, specific heat and electrical resistivity measurements. The heat capacity jump at Tc is ΔC/γTc = 1.41, confirming bulk superconductivity; the Sommerfeld coefficient γ = 4.1 mJ mol(-1) K(-2) and the Debye temperature ΘD = 157 K. The electron-phonon coupling strength is λel-ph = 0.59, and the thermodynamic critical field Hc is low, between 111 and 124 Oe CaBi2 is a moderate coupling type-I superconductor. Results of electronic structure calculations are reported and charge densities, electronic bands, densities of states and Fermi surfaces are discussed, focusing on the effects of spin-orbit coupling and electronic property anisotropy. We find a mixed quasi-2D + 3D character in the electronic structure, which reflects the layered crystal structure of the material.
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Affiliation(s)
- M J Winiarski
- Faculty of Applied Physics and Mathematics, Gdansk University of Technology, Narutowicza 11/12, 80-233 Gdansk, Poland.
| | - B Wiendlocha
- Faculty of Physics and Applied Computer Science, AGH University of Science and Technology, Aleja Mickiewicza 30, 30-059 Krakow, Poland
| | - S Gołąb
- Faculty of Physics and Applied Computer Science, AGH University of Science and Technology, Aleja Mickiewicza 30, 30-059 Krakow, Poland
| | - S K Kushwaha
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - P Wiśniewski
- Institute of Low Temperature and Structure Research, Polish Academy of Sciences, PNr 1410, 50-950 Wrocław, Poland
| | - D Kaczorowski
- Institute of Low Temperature and Structure Research, Polish Academy of Sciences, PNr 1410, 50-950 Wrocław, Poland
| | - J D Thompson
- Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - R J Cava
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - T Klimczuk
- Faculty of Applied Physics and Mathematics, Gdansk University of Technology, Narutowicza 11/12, 80-233 Gdansk, Poland.
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Kushwaha SK, Pletikosić I, Liang T, Gyenis A, Lapidus SH, Tian Y, Zhao H, Burch KS, Lin J, Wang W, Ji H, Fedorov AV, Yazdani A, Ong NP, Valla T, Cava RJ. Sn-doped Bi1.1Sb0.9Te2S bulk crystal topological insulator with excellent properties. Nat Commun 2016; 7:11456. [PMID: 27118032 PMCID: PMC4853473 DOI: 10.1038/ncomms11456] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 03/30/2016] [Indexed: 12/03/2022] Open
Abstract
A long-standing issue in topological insulator research has been to find a bulk single crystal material that provides a high-quality platform for characterizing topological surface states without interference from bulk electronic states. This material would ideally be a bulk insulator, have a surface state Dirac point energy well isolated from the bulk valence and conduction bands, display quantum oscillations from the surface state electrons and be growable as large, high-quality bulk single crystals. Here we show that this material obstacle is overcome by bulk crystals of lightly Sn-doped Bi1.1Sb0.9Te2S grown by the vertical Bridgman method. We characterize Sn-BSTS via angle-resolved photoemission spectroscopy, scanning tunnelling microscopy, transport studies, X-ray diffraction and Raman scattering. We present this material as a high-quality topological insulator that can be reliably grown as bulk single crystals and thus studied by many researchers interested in topological surface states. An ideal topological insulator possesses an insulating bulk and a unique conducting surface however such behaviour is typically inhibited by bulk conduction due to defects. Here, the authors show that Sn-doped Bi1.1Sb0.9Te2S grown by the vertical Bridgman technique might overcome this hurdle.
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Affiliation(s)
- S K Kushwaha
- Frick Chemistry Laboratory, Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
| | - I Pletikosić
- Department of Physics, Princeton University, Princeton, New Jersey 08544, USA.,Brookhaven National Laboratory, Condensed Matter Physics and Materials Science Department, Upton, New York 11973, USA
| | - T Liang
- Department of Physics, Princeton University, Princeton, New Jersey 08544, USA
| | - A Gyenis
- Department of Physics, Princeton University, Princeton, New Jersey 08544, USA
| | - S H Lapidus
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois 60439, USA
| | - Yao Tian
- Department of Physics, University of Toronto, Toronto, Ontario, Canada M5S 1A7
| | - He Zhao
- Department of Physics, Boston College, Boston, Massachusetts 02467-3804, USA
| | - K S Burch
- Department of Physics, Boston College, Boston, Massachusetts 02467-3804, USA
| | - Jingjing Lin
- Department of Physics, Princeton University, Princeton, New Jersey 08544, USA
| | - Wudi Wang
- Department of Physics, Princeton University, Princeton, New Jersey 08544, USA
| | - Huiwen Ji
- Frick Chemistry Laboratory, Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
| | - A V Fedorov
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Ali Yazdani
- Department of Physics, Princeton University, Princeton, New Jersey 08544, USA
| | - N P Ong
- Department of Physics, Princeton University, Princeton, New Jersey 08544, USA
| | - T Valla
- Brookhaven National Laboratory, Condensed Matter Physics and Materials Science Department, Upton, New York 11973, USA
| | - R J Cava
- Frick Chemistry Laboratory, Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
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Kushwaha SK, Krizan JW, Xiong J, Klimczuk T, Gibson QD, Liang T, Ong NP, Cava RJ. Superconducting properties and electronic structure of NaBi. J Phys Condens Matter 2014; 26:212201. [PMID: 24804822 DOI: 10.1088/0953-8984/26/21/212201] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Resistivity, dc magnetization, and heat capacity measurements are reported for superconducting NaBi. T(c), the electronic contribution to the specific heat γ, the ΔC(p)/γT(c) ratio, and the Debye temperature are found to be 2.15 K, 3.4 mJ mol(-1) K(-2), 0.78, and 140 K respectively. The calculated electron-phonon coupling constant (λ(ep) = 0.62) implies that NaBi is a moderately coupled superconductor. The upper critical field and coherence length are found to be 250 Oe and 115 nm, respectively. Electronic structure calculations show NaBi to be a good metal, in agreement with the experiments; the p(x) and p(y) orbitals of Bi dominate the electronic states at the Fermi Energy.
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Affiliation(s)
- S K Kushwaha
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
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Kushwaha SK, Sachan AS, Gupta A, Gupta R, Sharma RD. Efficacy and safety of unguided percutaneous fine needle aspiration cytology in peripheral lung lesions. J Indian Med Assoc 1996; 94:105-7. [PMID: 8810208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The efficacy and safety of unguided percutaneous fine needle aspiration cytology in peripheral lung lesions were studied in 42 patients. The diagnostic yield of unguided aspiration was 83.3%. The yield in malignant lesion was 85.7% while in benign lesion it was 78.6%. There was no false positive report. Complications seen were asymptomatic pneumothorax and blood tinged sputum in a few cases following aspiration. The procedure was well accepted by the patients. Unguided FNAC is a simple, quick, economical, safe and reliable procedure for the diagnosis of peripheral lung lesions.
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Affiliation(s)
- S K Kushwaha
- Department of Tuberculosis and Respiratory Diseases, SN Medical College, Agra
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