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Deschner D, Voordouw MJ, Fernando C, Campbell J, Waldner CL, Hill JE. Identification of genetic markers of resistance to macrolide class antibiotics in Mannheimia haemolytica isolates from a Saskatchewan feedlot. Appl Environ Microbiol 2024; 90:e0050224. [PMID: 38864630 PMCID: PMC11267883 DOI: 10.1128/aem.00502-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Accepted: 05/13/2024] [Indexed: 06/13/2024] Open
Abstract
Mannheimia haemolytica is a major contributor to bovine respiratory disease (BRD), which causes substantial economic losses to the beef industry, and there is an urgent need for rapid and accurate diagnostic tests to provide evidence for treatment decisions and support antimicrobial stewardship. Diagnostic sequencing can provide information about antimicrobial resistance genes in M. haemolytica more rapidly than conventional diagnostics. Realizing the full potential of diagnostic sequencing requires a comprehensive understanding of the genetic markers of antimicrobial resistance. We identified genetic markers of resistance in M. haemolytica to macrolide class antibiotics commonly used for control of BRD. Genome sequences were determined for 99 M. haemolytica isolates with six different susceptibility phenotypes collected over 2 years from a feedlot in Saskatchewan, Canada. Known macrolide resistance genes estT, msr(E), and mph(E) were identified in most resistant isolates within predicted integrative and conjugative elements (ICEs). ICE sequences lacking antibiotic resistance genes were detected in 10 of 47 susceptible isolates. No resistance-associated polymorphisms were detected in ribosomal RNA genes, although previously unreported mutations in the L22 and L23 ribosomal proteins were identified in 12 and 27 resistant isolates, respectively. Pangenome analysis led to the identification of 79 genes associated with resistance to gamithromycin, of which 95% (75 of 79) had no functional annotation. Most of the observed phenotypic resistance was explained by previously identified antibiotic resistance genes, although resistance to the macrolides gamithromycin and tulathromycin was not explained in 39 of 47 isolates, demonstrating the need for continued surveillance for novel determinants of macrolide resistance.IMPORTANCEBovine respiratory disease is the costliest disease of beef cattle in North America and the most common reason for injectable antibiotic use in beef cattle. Metagenomic sequencing offers the potential to make economically significant reductions in turnaround time for diagnostic information for evidence-based selection of antibiotics for use in the feedlot. The success of diagnostic sequencing depends on a comprehensive catalog of antimicrobial resistance genes and other genome features associated with reduced susceptibility. We analyzed the genome sequences of isolates of Mannheimia haemolytica, a major bovine respiratory disease pathogen, and identified both previously known and novel genes associated with reduced susceptibility to macrolide class antimicrobials. These findings reinforce the need for ongoing surveillance for markers of antimicrobial resistance to support improved diagnostics and antimicrobial stewardship.
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Affiliation(s)
- Darien Deschner
- Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, Canada
| | - Maarten J. Voordouw
- Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, Canada
| | - Champika Fernando
- Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, Canada
| | - John Campbell
- Department of Large Animal Clinical Sciences, University of Saskatchewan, Saskatoon, Canada
| | - Cheryl L. Waldner
- Department of Large Animal Clinical Sciences, University of Saskatchewan, Saskatoon, Canada
| | - Janet E. Hill
- Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, Canada
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da Silva Lima F, da Silva Gonçalves CE, Fock RA. A review of the role of zinc finger proteins on hematopoiesis. J Trace Elem Med Biol 2023; 80:127290. [PMID: 37659124 DOI: 10.1016/j.jtemb.2023.127290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 08/07/2023] [Accepted: 08/21/2023] [Indexed: 09/04/2023]
Abstract
The bone marrow is responsible for producing an incredible number of cells daily in order to maintain blood homeostasis through a process called hematopoiesis. Hematopoiesis is a greatly demanding process and one entirely dependent on complex interactions between the hematopoietic stem cell (HSC) and its surrounding microenvironment. Zinc (Zn2+) is considered an important trace element, playing diverse roles in different tissues and cell types, and zinc finger proteins (ZNF) are proteins that use Zn2+ as a structural cofactor. In this way, the ZNF structure is supported by a Zn2+ that coordinates many possible combinations of cysteine and histidine, with the most common ZNF being of the Cys2His2 (C2H2) type, which forms a family of transcriptional activators that play an important role in different cellular processes such as development, differentiation, and suppression, all of these being essential processes for an adequate hematopoiesis. This review aims to shed light on the relationship between ZNF and the regulation of the hematopoietic tissue. We include works with different designs, including both in vitro and in vivo studies, detailing how ZNF might regulate hematopoiesis.
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Affiliation(s)
- Fabiana da Silva Lima
- Department of Food and Experimental Nutrition, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | | | - Ricardo Ambrósio Fock
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil.
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Poignavent V, Hoh F, Terral G, Yang Y, Gillet FX, Kim JH, Allemand F, Lacombe E, Brugidou C, Cianferani S, Déméné H, Vignols F. A flexible and original architecture of two unrelated zinc fingers underlies the role of the multitask P1 in RYMV spread. J Mol Biol 2022; 434:167715. [DOI: 10.1016/j.jmb.2022.167715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 06/28/2022] [Accepted: 06/28/2022] [Indexed: 10/17/2022]
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Guo HJ, Wang LJ, Wang C, Guo DZ, Xu BH, Guo XQ, Li H. Identification of an Apis cerana zinc finger protein 41 gene and its involvement in the oxidative stress response. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2021; 108:e21830. [PMID: 34288081 DOI: 10.1002/arch.21830] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 06/17/2021] [Accepted: 06/18/2021] [Indexed: 06/13/2023]
Abstract
Zinc finger proteins (ZFPs) are a class of transcription factors that contain zinc finger domains and play important roles in growth, aging, and responses to abiotic and biotic stresses. These proteins activate or inhibit gene transcription by binding to single-stranded DNA or RNA and through RNA/DNA bidirectional binding and protein-protein interactions. However, few studies have focused on the oxidation resistance functions of ZFPs in insects, particularly Apis cerana. In the current study, we identified a ZFP41 gene from A. cerana, AcZFP41, and verified its function in oxidative stress responses. Real-time quantitative polymerase chain reaction showed that the transcription level of AcZFP41 was upregulated to different degrees during exposure to oxidative stress, including that induced by extreme temperature, UV radiation, or pesticides. In addition, the silencing of AcZFP41 led to changes in the expression patterns of some known antioxidant genes. Moreover, the activities of the antioxidant enzymes catalase (CAT), superoxide dismutase (SOD), peroxidase (POD), and glutathione S-transferase (GST) in AcZFP41-silenced honeybees were higher than those in a control group. In summary, the data indicate that AcZFP41 is involved in the oxidative stress response. The results provide a theoretical basis for further studies of zinc finger proteins and improve our understanding of the antioxidant mechanisms of honeybees.
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Affiliation(s)
- Hui-Juan Guo
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, China
| | - Li-Jun Wang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, China
| | - Chen Wang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, China
| | - De-Zheng Guo
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, China
| | - Bao-Hua Xu
- College of Animal Science and Technology, Shandong Agricultural University, Taian, Shandong, China
| | - Xing-Qi Guo
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, China
| | - Han Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, China
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Guérineau M, Bessa L, Moriau S, Lescop E, Bontems F, Mathy N, Guittet E, Bischerour J, Bétermier M, Morellet N. The unusual structure of the PiggyMac cysteine-rich domain reveals zinc finger diversity in PiggyBac-related transposases. Mob DNA 2021; 12:12. [PMID: 33926516 PMCID: PMC8086355 DOI: 10.1186/s13100-021-00240-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 03/09/2021] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Transposons are mobile genetic elements that colonize genomes and drive their plasticity in all organisms. DNA transposon-encoded transposases bind to the ends of their cognate transposons and catalyze their movement. In some cases, exaptation of transposon genes has allowed novel cellular functions to emerge. The PiggyMac (Pgm) endonuclease of the ciliate Paramecium tetraurelia is a domesticated transposase from the PiggyBac family. It carries a core catalytic domain typical of PiggyBac-related transposases and a short cysteine-rich domain (CRD), flanked by N- and C-terminal extensions. During sexual processes Pgm catalyzes programmed genome rearrangements (PGR) that eliminate ~ 30% of germline DNA from the somatic genome at each generation. How Pgm recognizes its DNA cleavage sites in chromatin is unclear and the structure-function relationships of its different domains have remained elusive. RESULTS We provide insight into Pgm structure by determining the fold adopted by its CRD, an essential domain required for PGR. Using Nuclear Magnetic Resonance, we show that the Pgm CRD binds two Zn2+ ions and forms an unusual binuclear cross-brace zinc finger, with a circularly permutated treble-clef fold flanked by two flexible arms. The Pgm CRD structure clearly differs from that of several other PiggyBac-related transposases, among which is the well-studied PB transposase from Trichoplusia ni. Instead, the arrangement of cysteines and histidines in the primary sequence of the Pgm CRD resembles that of active transposases from piggyBac-like elements found in other species and of human PiggyBac-derived domesticated transposases. We show that, unlike the PB CRD, the Pgm CRD does not bind DNA. Instead, it interacts weakly with the N-terminus of histone H3, whatever its lysine methylation state. CONCLUSIONS The present study points to the structural diversity of the CRD among transposases from the PiggyBac family and their domesticated derivatives, and highlights the diverse interactions this domain may establish with chromatin, from sequence-specific DNA binding to contacts with histone tails. Our data suggest that the Pgm CRD fold, whose unusual arrangement of cysteines and histidines is found in all PiggyBac-related domesticated transposases from Paramecium and Tetrahymena, was already present in the ancestral active transposase that gave rise to ciliate domesticated proteins.
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Affiliation(s)
- Marc Guérineau
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 1 Avenue de la Terrasse, 91198, Gif sur Yvette Cedex, France
| | - Luiza Bessa
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, 1 Avenue de la Terrasse, 91198, Gif sur Yvette Cedex, France
- Present addresses: Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 71 Avenue des Martyrs, 38000, Grenoble, France
| | - Séverine Moriau
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, 1 Avenue de la Terrasse, 91198, Gif sur Yvette Cedex, France
| | - Ewen Lescop
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, 1 Avenue de la Terrasse, 91198, Gif sur Yvette Cedex, France
| | - François Bontems
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, 1 Avenue de la Terrasse, 91198, Gif sur Yvette Cedex, France
| | - Nathalie Mathy
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 1 Avenue de la Terrasse, 91198, Gif sur Yvette Cedex, France
- Reproduction et Développement des Plantes UMR 5667, Ecole Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon Cedex 07, France
| | - Eric Guittet
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, 1 Avenue de la Terrasse, 91198, Gif sur Yvette Cedex, France
| | - Julien Bischerour
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 1 Avenue de la Terrasse, 91198, Gif sur Yvette Cedex, France
| | - Mireille Bétermier
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 1 Avenue de la Terrasse, 91198, Gif sur Yvette Cedex, France.
| | - Nelly Morellet
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, 1 Avenue de la Terrasse, 91198, Gif sur Yvette Cedex, France.
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Shahzad R, Jamil S, Ahmad S, Nisar A, Amina Z, Saleem S, Zaffar Iqbal M, Muhammad Atif R, Wang X. Harnessing the potential of plant transcription factors in developing climate resilient crops to improve global food security: Current and future perspectives. Saudi J Biol Sci 2021; 28:2323-2341. [PMID: 33911947 PMCID: PMC8071895 DOI: 10.1016/j.sjbs.2021.01.028] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 12/09/2020] [Accepted: 01/12/2021] [Indexed: 12/20/2022] Open
Abstract
Crop plants should be resilient to climatic factors in order to feed ever-increasing populations. Plants have developed stress-responsive mechanisms by changing their metabolic pathways and switching the stress-responsive genes. The discovery of plant transcriptional factors (TFs), as key regulators of different biotic and abiotic stresses, has opened up new horizons for plant scientists. TFs perceive the signal and switch certain stress-responsive genes on and off by binding to different cis-regulatory elements. More than 50 families of plant TFs have been reported in nature. Among them, DREB, bZIP, MYB, NAC, Zinc-finger, HSF, Dof, WRKY, and NF-Y are important with respect to biotic and abiotic stresses, but the potential of many TFs in the improvement of crops is untapped. In this review, we summarize the role of different stress-responsive TFs with respect to biotic and abiotic stresses. Further, challenges and future opportunities linked with TFs for developing climate-resilient crops are also elaborated.
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Affiliation(s)
- Rahil Shahzad
- Agricultural Biotechnology Research Institute, Ayub Agricultural Research Institute, Faisalabad 38000, Pakistan
| | - Shakra Jamil
- Agricultural Biotechnology Research Institute, Ayub Agricultural Research Institute, Faisalabad 38000, Pakistan
| | - Shakeel Ahmad
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Amina Nisar
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad 38000, Pakistan
| | - Zarmaha Amina
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad 38000, Pakistan
| | - Shazmina Saleem
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad 38000, Pakistan
| | - Muhammad Zaffar Iqbal
- Agricultural Biotechnology Research Institute, Ayub Agricultural Research Institute, Faisalabad 38000, Pakistan
| | - Rana Muhammad Atif
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad 38000, Pakistan
- Center for Advanced Studies in Agriculture and Food Security (CAS-AFS), University of Agriculture Faisalabad, University Road, 38040, Faisalabad, Pakistan
| | - Xiukang Wang
- College of Life Sciences, Yan’an University, Yan’an 716000, China
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Talar U, Kiełbowicz-Matuk A. Beyond Arabidopsis: BBX Regulators in Crop Plants. Int J Mol Sci 2021; 22:ijms22062906. [PMID: 33809370 PMCID: PMC7999331 DOI: 10.3390/ijms22062906] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 03/08/2021] [Accepted: 03/09/2021] [Indexed: 01/16/2023] Open
Abstract
B-box proteins represent diverse zinc finger transcription factors and regulators forming large families in various plants. A unique domain structure defines them—besides the highly conserved B-box domains, some B-box (BBX) proteins also possess CCT domain and VP motif. Based on the presence of these specific domains, they are mostly classified into five structural groups. The particular members widely differ in structure and fulfill distinct functions in regulating plant growth and development, including seedling photomorphogenesis, the anthocyanins biosynthesis, photoperiodic regulation of flowering, and hormonal pathways. Several BBX proteins are additionally involved in biotic and abiotic stress response. Overexpression of some BBX genes stimulates various stress-related genes and enhanced tolerance to different stresses. Moreover, there is evidence of interplay between B-box and the circadian clock mechanism. This review highlights the role of BBX proteins as a part of a broad regulatory network in crop plants, considering their participation in development, physiology, defense, and environmental constraints. A description is also provided of how various BBX regulators involved in stress tolerance were applied in genetic engineering to obtain stress tolerance in transgenic crops.
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The Novel Halovirus Hardycor1, and the Presence of Active (Induced) Proviruses in Four Haloarchaea. Genes (Basel) 2021; 12:genes12020149. [PMID: 33498646 PMCID: PMC7911831 DOI: 10.3390/genes12020149] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/18/2021] [Accepted: 01/20/2021] [Indexed: 12/15/2022] Open
Abstract
The virus Hardycor1 was isolated in 1998 and infects the haloarchaeon Halorubrum coriense. DNA from a frozen stock (HC1) was sequenced and the viral genome found to be 45,142 bp of dsDNA, probably having redundant, circularly permuted termini. The genome showed little similarity (BLASTn) to known viruses. Only twenty-two of the 53 (41%) predicted proteins were significantly similar to sequences in the NCBI nr protein database (E-value ≤ 10-15). Six caudovirus-like proteins were encoded, including large subunit terminase (TerL), major capsid protein (Mcp) and tape measure protein (Tmp). Hardycor1 was predicted to be a siphovirus (VIRFAM). No close relationship to other viruses was found using phylogenetic tree reconstructions based on TerL and Mcp. Unexpectedly, the sequenced virus stock HC1 also revealed two induced proviruses of the host: a siphovirus (Humcor1) and a pleolipovirus (Humcor2). A re-examination of other similarly sequenced, archival virus stocks revealed induced proviruses of Haloferax volcanii, Haloferax gibbonsii and Haloarcula hispanica, three of which were pleolipoviruses. One provirus (Halfvol2) of Hfx. volcanii showed little similarity (BLASTn) to known viruses and probably represents a novel virus group. The attP sequences of many pleolipoproviruses were found to be embedded in a newly detected coding sequence, split in the provirus state, that spans between genes for integrase and a downstream CxxC-motif protein. This gene might play an important role in regulation of the temperate state.
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Negishi M, Kobayashi K, Sakuma T, Sueyoshi T. Nuclear receptor phosphorylation in xenobiotic signal transduction. J Biol Chem 2020; 295:15210-15225. [PMID: 32788213 DOI: 10.1074/jbc.rev120.007933] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 08/05/2020] [Indexed: 12/11/2022] Open
Abstract
Nuclear pregnane X receptor (PXR, NR1I2) and constitutive active/androstane receptor (CAR, NR1I3) are nuclear receptors characterized in 1998 by their capability to respond to xenobiotics and activate cytochrome P450 (CYP) genes. An anti-epileptic drug, phenobarbital (PB), activates CAR and its target CYP2B genes, whereas PXR is activated by drugs such as rifampicin and statins for the CYP3A genes. Inevitably, both nuclear receptors have been investigated as ligand-activated nuclear receptors by identifying and characterizing xenobiotics and therapeutics that directly bind CAR and/or PXR to activate them. However, PB, which does not bind CAR directly, presented an alternative research avenue for an indirect ligand-mediated nuclear receptor activation mechanism: phosphorylation-mediated signal regulation. This review summarizes phosphorylation-based mechanisms utilized by xenobiotics to elicit cell signaling. First, the review presents how PB activates CAR (and other nuclear receptors) through a conserved phosphorylation motif located between two zinc fingers within its DNA-binding domain. PB-regulated phosphorylation at this motif enables nuclear receptors to form communication networks, integrating their functions. Next, the review discusses xenobiotic-induced PXR activation in the absence of the conserved DNA-binding domain phosphorylation motif. In this case, phosphorylation occurs at a motif located within the ligand-binding domain to transduce cell signaling that regulates hepatic energy metabolism. Finally, the review delves into the implications of xenobiotic-induced signaling through phosphorylation in disease development and progression.
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Affiliation(s)
- Masahiko Negishi
- Pharmacogenetics Section, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA.
| | - Kaoru Kobayashi
- Department of Biopharmaceutics, Meiji Pharmaceutical University, Kiyose, Tokyo, Japan
| | - Tsutomu Sakuma
- School of Pharmaceutical Sciences, Ohu University, Koriyama, Fukushima, Japan
| | - Tatsuya Sueyoshi
- Pharmacogenetics Section, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA
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Comparative Genomics of Two New HF1-like Haloviruses. Genes (Basel) 2020; 11:genes11040405. [PMID: 32276506 PMCID: PMC7230728 DOI: 10.3390/genes11040405] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 04/03/2020] [Accepted: 04/06/2020] [Indexed: 12/14/2022] Open
Abstract
Few genomes of the HF1-group of viruses are currently available, and further examples would enhance the understanding of their evolution, improve their gene annotation, and assist in understanding gene function and regulation. Two novel HF1-group haloviruses, Serpecor1 and Hardycor2, were recovered from widely separated hypersaline lakes in Australia. Both are myoviruses with linear dsDNA genomes and infect the haloarchaeon Halorubrum coriense. Both genomes possess long, terminal direct repeat (TDR) sequences (320 bp for Serpecor1 and 306 bp for Hardycor2). The Serpecor1 genome is 74,196 bp in length, 57.0% G+C, and has 126 annotated coding sequences (CDS). Hardycor2 has a genome of 77,342 bp, 55.6% G+C, and 125 annotated CDS. They show high nucleotide sequence similarity to each other (78%) and with HF1 (>75%), and carry similar intergenic repeat (IR) sequences to those originally described in HF1 and HF2. Hardycor2 carries a DNA methyltransferase gene in the same genomic neighborhood as the methyltransferase genes of HF1, HF2 and HRTV-5, but is in the opposite orientation, and the inferred proteins are only distantly related. Comparative genomics allowed us to identify the candidate genes mediating cell attachment. The genomes of Serpecor1 and Hardycor2 encode numerous small proteins carrying one or more CxxC motifs, a signature feature of zinc-finger domain proteins that are known to participate in diverse biomolecular interactions.
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Li G, Ma X, Xu L. The roles of zinc finger proteins in non-alcoholic fatty liver disease. LIVER RESEARCH 2020. [DOI: 10.1016/j.livres.2020.01.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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12
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Smirnova J, Kabin E, Tõugu V, Palumaa P. Redox properties of Cys 2His 2 and Cys 4 zinc fingers determined by electrospray ionization mass spectrometry. FEBS Open Bio 2018; 8:923-931. [PMID: 29928572 PMCID: PMC5985984 DOI: 10.1002/2211-5463.12422] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 03/12/2018] [Accepted: 03/23/2018] [Indexed: 01/05/2023] Open
Abstract
Zinc finger (ZF) protein motifs, stabilized by binding of Zn(II), typically function as interaction modules that bind nucleic acids, proteins and other molecules. The elucidation of the redox states of ZF proteins in cellular conditions, which depend on their midpoint redox potentials, is important for understanding of ZF functioning. In the present study we determined the midpoint redox potentials for representatives of Cys2His2 and Cys4 types of ZF proteins in apo and Zn(II)-bound forms using electrospray ionization mass spectrometry. The midpoint redox potentials of the apo forms of Cys2His2 and Cys4 ZF proteins were -326 and -365 mV (pH 7.5), respectively. These values are close to the cytosolic redox potential of approx. -350 mV (pH 7.5) and thus we can conclude that the apo form of Cys2His2-type ZF proteins is predominantly reduced but apo forms of Cys4-type ZF proteins should be substantially oxidized in the cytoplasm. As expected, Zn(II) binding stabilized the reduced forms of both ZF proteins: the corresponding redox potential values were -284 and -301 mV, respectively. Consequently, binding of Zn(II) ions to ZF motifs can act as a sensitive switch that activates the functioning of the ZF motifs within the cell, and also protects them from oxidation and can function as part of a redox-sensitive regulation mechanism of cellular functions.
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Affiliation(s)
- Julia Smirnova
- Department of Chemistry and Biotechnology Tallinn University of Technology Estonia
| | - Ekaterina Kabin
- Department of Chemistry and Biotechnology Tallinn University of Technology Estonia
| | - Vello Tõugu
- Department of Chemistry and Biotechnology Tallinn University of Technology Estonia
| | - Peep Palumaa
- Department of Chemistry and Biotechnology Tallinn University of Technology Estonia
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Evolutionary convergence and divergence in archaeal chromosomal proteins and Chromo-like domains from bacteria and eukaryotes. Sci Rep 2018; 8:6196. [PMID: 29670199 PMCID: PMC5906684 DOI: 10.1038/s41598-018-24467-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 04/04/2018] [Indexed: 11/08/2022] Open
Abstract
SH3-fold-β-barrel domains of the chromo-like superfamily recognize epigenetic marks in eukaryotic proteins. Their provenance has been placed either in archaea, based on apparent structural similarity to chromatin-compacting Sul7d and Cren7 proteins, or in bacteria based on the presence of sequence homologs. Using sequence and structural evidence we establish that the archaeal Cren7/Sul7 proteins emerged from a zinc ribbon (ZnR) ancestor. Further, we show that the ancestral eukaryotic chromo-like domains evolved from bacterial versions, likely acquired from early endosymbioses, which already possessed an aromatic cage for recognition of modified amino-groups. These bacterial versions are part of a radiation of secreted SH3-fold domains, which spawned both chromo-like domains and classical SH3 domains in the context of peptide-recognition in the peptidoglycan or the extracellular matrix. This establishes that Cren7/Sul7 converged to a “SH3”-like state from a ZnR precursor via the loss of metal-chelation and acquisition of stronger hydrophobic interactions; it is unlikely to have participated in the evolution of the chromo-like domains. We show that archaea possess several Cren7/Sul7-related proteins with intact Zn-chelating ligands, which we predict to play previously unstudied roles in chromosome segregation during cell-division comparable to the PRC barrel and CdvA domain proteins.
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Martínez-Lumbreras S, Alfano C, Evans NJ, Collins KM, Flanagan KA, Atkinson RA, Krysztofinska EM, Vydyanath A, Jackter J, Fixon-Owoo S, Camp AH, Isaacson RL. Structural and Functional Insights into Bacillus subtilis Sigma Factor Inhibitor, CsfB. Structure 2018; 26:640-648.e5. [PMID: 29526435 PMCID: PMC5890618 DOI: 10.1016/j.str.2018.02.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 11/17/2017] [Accepted: 02/06/2018] [Indexed: 11/23/2022]
Abstract
Global changes in bacterial gene expression can be orchestrated by the coordinated activation/deactivation of alternative sigma (σ) factor subunits of RNA polymerase. Sigma factors themselves are regulated in myriad ways, including via anti-sigma factors. Here, we have determined the solution structure of anti-sigma factor CsfB, responsible for inhibition of two alternative sigma factors, σG and σE, during spore formation by Bacillus subtilis. CsfB assembles into a symmetrical homodimer, with each monomer bound to a single Zn2+ ion via a treble-clef zinc finger fold. Directed mutagenesis indicates that dimer formation is critical for CsfB-mediated inhibition of both σG and σE, and we have characterized these interactions in vitro. This work represents an advance in our understanding of how CsfB mediates inhibition of two alternative sigma factors to drive developmental gene expression in a bacterium.
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MESH Headings
- Amino Acid Sequence
- Bacillus subtilis/chemistry
- Bacillus subtilis/genetics
- Bacillus subtilis/metabolism
- Binding Sites
- Cations, Divalent
- Cloning, Molecular
- Crystallography, X-Ray
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Gene Expression Regulation, Bacterial
- Genetic Vectors/chemistry
- Genetic Vectors/metabolism
- Models, Molecular
- Mutation
- Protein Binding
- Protein Conformation, alpha-Helical
- Protein Conformation, beta-Strand
- Protein Interaction Domains and Motifs
- Protein Isoforms/antagonists & inhibitors
- Protein Isoforms/chemistry
- Protein Isoforms/genetics
- Protein Isoforms/metabolism
- Protein Multimerization
- Recombinant Proteins/chemistry
- Recombinant Proteins/genetics
- Recombinant Proteins/metabolism
- Repressor Proteins/chemistry
- Repressor Proteins/genetics
- Repressor Proteins/metabolism
- Sequence Alignment
- Sequence Homology, Amino Acid
- Sigma Factor/antagonists & inhibitors
- Sigma Factor/chemistry
- Sigma Factor/genetics
- Sigma Factor/metabolism
- Spores, Bacterial/chemistry
- Spores, Bacterial/genetics
- Spores, Bacterial/metabolism
- Zinc/chemistry
- Zinc/metabolism
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Affiliation(s)
| | - Caterina Alfano
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London SE1 1DB, UK; Structural Biology and Biophysics Unit, Fondazione Ri.MED, Via Bandiera, 11, 90133 Palermo, Italy
| | - Nicola J Evans
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London SE1 1DB, UK
| | - Katherine M Collins
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London SE1 1DB, UK
| | - Kelly A Flanagan
- Department of Biological Sciences, Mount Holyoke College, 50 College Street, South Hadley, MA 01075, USA
| | - R Andrew Atkinson
- Centre for Biomolecular Spectroscopy and Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, UK
| | - Ewelina M Krysztofinska
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London SE1 1DB, UK
| | - Anupama Vydyanath
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London SE1 1DB, UK
| | - Jacquelin Jackter
- Department of Biological Sciences, Mount Holyoke College, 50 College Street, South Hadley, MA 01075, USA
| | - Sarah Fixon-Owoo
- Department of Biological Sciences, Mount Holyoke College, 50 College Street, South Hadley, MA 01075, USA
| | - Amy H Camp
- Department of Biological Sciences, Mount Holyoke College, 50 College Street, South Hadley, MA 01075, USA
| | - Rivka L Isaacson
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London SE1 1DB, UK.
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15
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Structural Insights in Multifunctional Papillomavirus Oncoproteins. Viruses 2018; 10:v10010037. [PMID: 29342959 PMCID: PMC5795450 DOI: 10.3390/v10010037] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Revised: 01/10/2018] [Accepted: 01/11/2018] [Indexed: 02/08/2023] Open
Abstract
Since their discovery in the mid-eighties, the main papillomavirus oncoproteins E6 and E7 have been recalcitrant to high-resolution structure analysis. However, in the last decade a wealth of three-dimensional information has been gained on both proteins whether free or complexed to host target proteins. Here, we first summarize the diverse activities of these small multifunctional oncoproteins. Next, we review the available structural data and the new insights they provide about the evolution of E6 and E7, their multiple interactions and their functional variability across human papillomavirus (HPV) species.
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16
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Jablonska J, Matelska D, Steczkiewicz K, Ginalski K. Systematic classification of the His-Me finger superfamily. Nucleic Acids Res 2017; 45:11479-11494. [PMID: 29040665 PMCID: PMC5714182 DOI: 10.1093/nar/gkx924] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 09/29/2017] [Indexed: 02/06/2023] Open
Abstract
The His-Me finger endonucleases, also known as HNH or ββα-metal endonucleases, form a large and diverse protein superfamily. The His-Me finger domain can be found in proteins that play an essential role in cells, including genome maintenance, intron homing, host defense and target offense. Its overall structural compactness and non-specificity make it a perfectly-tailored pathogenic module that participates on both sides of inter- and intra-organismal competition. An extremely low sequence similarity across the superfamily makes it difficult to identify and classify new His-Me fingers. Using state-of-the-art distant homology detection methods, we provide an updated and systematic classification of His-Me finger proteins. In this work, we identified over 100 000 proteins and clustered them into 38 groups, of which three groups are new and cannot be found in any existing public domain database of protein families. Based on an analysis of sequences, structures, domain architectures, and genomic contexts, we provide a careful functional annotation of the poorly characterized members of this superfamily. Our results may inspire further experimental investigations that should address the predicted activity and clarify the potential substrates, to provide more detailed insights into the fundamental biological roles of these proteins.
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Affiliation(s)
- Jagoda Jablonska
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland
| | - Dorota Matelska
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland
| | - Kamil Steczkiewicz
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland
| | - Krzysztof Ginalski
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland
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