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Abstract
Dickeya dadantii is a phytopathogenic bacterium that causes soft rot in a wide range of plant hosts worldwide and a model organism for studying virulence gene regulation. The present study provides a comprehensive and annotated transcriptomic map of D. dadantii obtained by a computational method combining five independent transcriptomic data sets: (i) paired-end RNA sequencing (RNA-seq) data for a precise reconstruction of the RNA landscape; (ii) DNA microarray data providing transcriptional responses to a broad variety of environmental conditions; (iii) long-read Nanopore native RNA-seq data for isoform-level transcriptome validation and determination of transcription termination sites; (iv) differential RNA sequencing (dRNA-seq) data for the precise mapping of transcription start sites; (v) in planta DNA microarray data for a comparison of gene expression profiles between in vitro experiments and the early stages of plant infection. Our results show that transcription units sometimes coincide with predicted operons but are generally longer, most of them comprising internal promoters and terminators that generate alternative transcripts of variable gene composition. We characterize the occurrence of transcriptional read-through at terminators, which might play a basal regulation role and explain the extent of transcription beyond the scale of operons. We finally highlight the presence of noncontiguous operons and excludons in the D. dadantii genome, novel genomic arrangements that might contribute to the basal coordination of transcription. The highlighted transcriptional organization may allow D. dadantii to finely adjust its gene expression program for a rapid adaptation to fast-changing environments.
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Wang Y, Huang JM, Zhou YL, Almeida A, Finn RD, Danchin A, He LS. Phylogenomics of expanding uncultured environmental Tenericutes provides insights into their pathogenicity and evolutionary relationship with Bacilli. BMC Genomics 2020; 21:408. [PMID: 32552739 PMCID: PMC7301438 DOI: 10.1186/s12864-020-06807-4] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 06/05/2020] [Indexed: 12/28/2022] Open
Abstract
Background The metabolic capacity, stress response and evolution of uncultured environmental Tenericutes have remained elusive, since previous studies have been largely focused on pathogenic species. In this study, we expanded analyses on Tenericutes lineages that inhabit various environments using a collection of 840 genomes. Results Several environmental lineages were discovered inhabiting the human gut, ground water, bioreactors and hypersaline lake and spanning the Haloplasmatales and Mycoplasmatales orders. A phylogenomics analysis of Bacilli and Tenericutes genomes revealed that some uncultured Tenericutes are affiliated with novel clades in Bacilli, such as RF39, RFN20 and ML615. Erysipelotrichales and two major gut lineages, RF39 and RFN20, were found to be neighboring clades of Mycoplasmatales. We detected habitat-specific functional patterns between the pathogenic, gut and the environmental Tenericutes, where genes involved in carbohydrate storage, carbon fixation, mutation repair, environmental response and amino acid cleavage are overrepresented in the genomes of environmental lineages, perhaps as a result of environmental adaptation. We hypothesize that the two major gut lineages, namely RF39 and RFN20, are probably acetate and hydrogen producers. Furthermore, deteriorating capacity of bactoprenol synthesis for cell wall peptidoglycan precursors secretion is a potential adaptive strategy employed by these lineages in response to the gut environment. Conclusions This study uncovers the characteristic functions of environmental Tenericutes and their relationships with Bacilli, which sheds new light onto the pathogenicity and evolutionary processes of Mycoplasmatales.
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Affiliation(s)
- Yong Wang
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, No. 28, Luhuitou Road, Sanya, Hai Nan, P.R. China.
| | - Jiao-Mei Huang
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, No. 28, Luhuitou Road, Sanya, Hai Nan, P.R. China.,University of Chinese Academy of Sciences, Beijing, China
| | - Ying-Li Zhou
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, No. 28, Luhuitou Road, Sanya, Hai Nan, P.R. China.,University of Chinese Academy of Sciences, Beijing, China
| | - Alexandre Almeida
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK.,Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Robert D Finn
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
| | - Antoine Danchin
- Kodikos, Department of Infection, Immunity and Inflammation, Institut Cochin INSERM U1016 - CNRS UMR8104 - Université Paris Descartes, 24 rue du Faubourg Saint-Jacques, 75014, Paris, France.,Li Kashing Faculty of Medicine, School of Biomedical Sciences, University of Hong Kong, 21 Sassoon Road, Hong Kong, SAR, China
| | - Li-Sheng He
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, No. 28, Luhuitou Road, Sanya, Hai Nan, P.R. China
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Sakai Y, Miyauchi K, Kimura S, Suzuki T. Biogenesis and growth phase-dependent alteration of 5-methoxycarbonylmethoxyuridine in tRNA anticodons. Nucleic Acids Res 2015; 44:509-23. [PMID: 26681692 PMCID: PMC4737166 DOI: 10.1093/nar/gkv1470] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 12/02/2015] [Indexed: 12/22/2022] Open
Abstract
Post-transcriptional modifications at the anticodon first (wobble) position of tRNA play critical roles in precise decoding of genetic codes. 5-carboxymethoxyuridine (cmo5U) and its methyl ester derivative 5-methoxycarbonylmethoxyuridine (mcmo5U) are modified nucleosides found at the anticodon wobble position in several tRNAs from Gram-negative bacteria. cmo5U and mcmo5U facilitate non-Watson–Crick base pairing with guanosine and pyrimidines at the third positions of codons, thereby expanding decoding capabilities. By mass spectrometric analyses of individual tRNAs and a shotgun approach of total RNA from Escherichia coli, we identified mcmo5U as a major modification in tRNAAla1, tRNASer1, tRNAPro3 and tRNAThr4; by contrast, cmo5U was present primarily in tRNALeu3 and tRNAVal1. In addition, we discovered 5-methoxycarbonylmethoxy-2′-O-methyluridine (mcmo5Um) as a novel but minor modification in tRNASer1. Terminal methylation frequency of mcmo5U in tRNAPro3 was low (≈30%) in the early log phase of cell growth, gradually increased as growth proceeded and reached nearly 100% in late log and stationary phases. We identified CmoM (previously known as SmtA), an AdoMet-dependent methyltransferase that methylates cmo5U to form mcmo5U. A luciferase reporter assay based on a +1 frameshift construct revealed that terminal methylation of mcmo5U contributes to the decoding ability of tRNAAla1.
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Affiliation(s)
- Yusuke Sakai
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Kenjyo Miyauchi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Satoshi Kimura
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
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Rybenkov VV, Herrera V, Petrushenko ZM, Zhao H. MukBEF, a chromosomal organizer. J Mol Microbiol Biotechnol 2015; 24:371-83. [PMID: 25732339 DOI: 10.1159/000369099] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Global folding of bacterial chromosome requires the activity of condensins. These highly conserved proteins are involved in various aspects of higher-order chromatin dynamics in a diverse range of organisms. Two distinct superfamilies of condensins have been identified in bacteria. The SMC-ScpAB proteins bear significant homology to eukaryotic condensins and cohesins and are found in most of the presently sequenced bacteria. This review focuses on the MukBEF/MksBEF superfamily, which is broadly distributed across diverse bacteria and is characterized by low sequence conservation. The prototypical member of this superfamily, the Escherichia coli condensin MukBEF, continues to provide critical insights into the mechanism of the proteins. MukBEF acts as a complex molecular machine that assists in chromosome segregation and global organization. The review focuses on the mechanistic analysis of DNA organization by MukBEF with emphasis on its involvement in the formation of chromatin scaffold and plausible other roles in chromosome segregation.
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Affiliation(s)
- Valentin V Rybenkov
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Okla., USA
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She W, Wang Q, Mordukhova EA, Rybenkov VV. MukEF Is required for stable association of MukB with the chromosome. J Bacteriol 2007; 189:7062-8. [PMID: 17644586 PMCID: PMC2045213 DOI: 10.1128/jb.00770-07] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
MukB is a bacterial SMC(structural maintenance of chromosome) protein required for correct folding of the Escherichia coli chromosome. MukB acts in complex with the two non-SMC proteins, MukE and MukF. The role of MukEF is unclear. MukEF disrupts MukB-DNA interactions in vitro. In vivo, however, MukEF stimulates MukB-induced DNA condensation and is required for the assembly of MukB clusters at the quarter positions of the cell length. We report here that MukEF is essential for stable association of MukB with the chromosome. We found that MukBEF forms a stable complex with the chromosome that copurifies with nucleoids following gentle cell lysis. Little MukB could be found with the nucleoids in the absence or upon overproduction of MukEF. Similarly, overproduced MukEF recruited MukB-green fluorescent protein (GFP) from its quarter positions, indicating that formation of MukB-GFP clusters and stable association with the chromosome could be mechanistically related. Finally, we report that MukE-GFP forms foci at the quarter positions of the cell length but not in cells that lack MukB or overproduce MukEF, suggesting that the clusters are formed by MukBEF and not by its individual subunits. These data support the view that MukBEF acts as a macromolecular assembly, a scaffold, in chromosome organization and that MukEF is essential for the assembly of this scaffold.
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Affiliation(s)
- Weifeng She
- Department of Chemistry and Biochemistry, University of Oklahoma, 620 Parrington Oval, Norman, OK 73019, USA
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Seshasayee ASN. An assessment of the role of DNA adenine methyltransferase on gene expression regulation in E coli. PLoS One 2007; 2:e273. [PMID: 17342207 PMCID: PMC1804101 DOI: 10.1371/journal.pone.0000273] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2006] [Accepted: 02/14/2007] [Indexed: 11/19/2022] Open
Abstract
N6-Adenine methylation is an important epigenetic signal, which regulates various processes, such as DNA replication and repair and transcription. In γ-proteobacteria, Dam is a stand-alone enzyme that methylates GATC sites, which are non-randomly distributed in the genome. Some of these overlap with transcription factor binding sites. This work describes a global computational analysis of a published Dam knockout microarray alongside other publicly available data to throw insights into the extent to which Dam regulates transcription by interfering with protein binding. The results indicate that DNA methylation by DAM may not globally affect gene transcription by physically blocking access of transcription factors to binding sites. Down-regulation of Dam during stationary phase correlates with the activity of TFs whose binding sites are enriched for GATC sites.
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Affiliation(s)
- Aswin Sai Narain Seshasayee
- Genomics and Regulatory Systems Group, EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom.
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Wang Q, Mordukhova EA, Edwards AL, Rybenkov VV. Chromosome condensation in the absence of the non-SMC subunits of MukBEF. J Bacteriol 2006; 188:4431-41. [PMID: 16740950 PMCID: PMC1482961 DOI: 10.1128/jb.00313-06] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
MukBEF is a bacterial SMC (structural maintenance of chromosome) complex required for chromosome partitioning in Escherichia coli. We report that overproduction of MukBEF results in marked chromosome condensation. This condensation is rapid and precedes the effects of overproduction on macromolecular synthesis. Condensed nucleoids are often mispositioned; however, cell viability is only mildly affected. The overproduction of MukB leads to a similar chromosome condensation, even in the absence of MukE and MukF. Thus, the non-SMC subunits of MukBEF play only an auxiliary role in chromosome condensation. MukBEF, however, was often a better condensin than MukB. Furthermore, the chromosome condensation by MukB did not rescue the temperature sensitivity of MukEF-deficient cells, nor did it suppress the high frequency of anucleate cell formation. We infer that the role of MukBEF in stabilizing chromatin architecture is more versatile than its role in controlling chromosome size. We further propose that MukBEF could be directly involved in chromosome segregation.
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Affiliation(s)
- Qinhong Wang
- University of Oklahoma, Department of Chemistry and Biochemistry, 620 Parrington Oval, Norman, OK 73019, USA
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Abstract
Plasmid-encoded partition genes determine the dynamic localization of plasmid molecules from the mid-cell position to the 1/4 and 3/4 positions. Similarly, bacterial homologs of the plasmid genes participate in controlling the bidirectional migration of the replication origin (oriC) regions during sporulation and vegetative growth in Bacillus subtilis, but not in Escherichia coli. In E. coli, but not B. subtilis, the chromosomal DNA is fully methylated by DNA adenine methyltransferase. The E. coli SeqA protein, which binds preferentially to hemimethylated nascent DNA strands, exists as discrete foci in vivo. A single SeqA focus, which is a SeqA-hemimethylated DNA cluster, splits into two foci that then abruptly migrate bidirectionally to the 1/4 and 3/4 positions during replication. Replicated oriC copies are linked to each other for a substantial period of generation time, before separating from each other and migrating in opposite directions. The MukFEB complex of E. coli and Smc of B. subtilis appear to participate in the reorganization of bacterial sister chromosomes.
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Affiliation(s)
- S Hiraga
- Department of Molecular Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kuhonji 4-24-1, Kumamoto 862-0976, Japan.
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Abstract
This map is an update of the edition 9 map by Berlyn et al. (M. K. B. Berlyn, K. B. Low, and K. E. Rudd, p. 1715-1902, in F. C. Neidhardt et al., ed., Escherichia coli and Salmonella: cellular and molecular biology, 2nd ed., vol. 2, 1996). It uses coordinates established by the completed sequence, expressed as 100 minutes for the entire circular map, and adds new genes discovered and established since 1996 and eliminates those shown to correspond to other known genes. The latter are included as synonyms. An alphabetical list of genes showing map location, synonyms, the protein or RNA product of the gene, phenotypes of mutants, and reference citations is provided. In addition to genes known to correspond to gene sequences, other genes, often older, that are described by phenotype and older mapping techniques and that have not been correlated with sequences are included.
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Affiliation(s)
- M K Berlyn
- Department of Biology and School of Forestry and Environmental Studies, Yale University, New Haven, Connecticut 06520-8104, USA.
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Kido M, Yamanaka K, Mitani T, Niki H, Ogura T, Hiraga S. RNase E polypeptides lacking a carboxyl-terminal half suppress a mukB mutation in Escherichia coli. J Bacteriol 1996; 178:3917-25. [PMID: 8682798 PMCID: PMC232654 DOI: 10.1128/jb.178.13.3917-3925.1996] [Citation(s) in RCA: 126] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
We have isolated suppressor mutants that suppress temperature-sensitive colony formation and anucleate cell production of a mukB mutation. A linkage group (smbB) of the suppressor mutations is located in the rne/ams/hmp gene encoding the processing endoribonuclease RNase E. All of the rne (smbB) mutants code for truncated RNase E polypeptides lacking a carboxyl-terminal half. The amount of MukB protein was higher in these rne mutants than that in the rne+ strain. These rne mutants grew nearly normally in the mukB+ genetic background. The copy number of plasmid pBR322 in these rne mutants was lower than that in the rne+ isogenic strain. The results suggest that these rne mutations increase the half-lives of mukB mRNA and RNAI of pBR322, the antisense RNA regulating ColE1-type plasmid replication. We have demonstrated that the wild-type RNase E protein bound to polynucleotide phosphorylase (PNPase) but a truncated RNase E polypeptide lacking the C-terminal half did not. We conclude that the C-terminal half of RNase E is not essential for viability but plays an important role for binding with PNPase. RNase E and PNPase of the multiprotein complex presumably cooperate for effective processing and turnover of specific substrates, such as mRNAs and other RNAs in vivo.
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Affiliation(s)
- M Kido
- Department of Molecular Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University School of Medicine, Kumamoto, Japan
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Yamanaka K, Ogura T, Niki H, Hiraga S. Identification of two new genes, mukE and mukF, involved in chromosome partitioning in Escherichia coli. MOLECULAR & GENERAL GENETICS : MGG 1996; 250:241-51. [PMID: 8602138 DOI: 10.1007/bf02174381] [Citation(s) in RCA: 70] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
We have previously reported that the MukB protein is essential for chromosome partitioning in Escherichia coli and that mukB mutants produce anucleate cells and are temperature-sensitive for colony formation. The mukB gene maps at 21 min on the E. coli chromosome and smtA-mukF-mukE-mukB genes might comprise an operon, which is transcribed in a clockwise direction. Here, we report that mukF and mukE null mutants are both temperature-sensitive for colony formation and produce anucleate cells even at the permissive temperature. These phenotypes are the same as those observed in the mukB null mutant. The primary sequence of MukF includes a leucine zipper structure and an acidic domain. Mutational analysis revealed that both are required for MukF function. When the MukF protein was overproduced in the wild-type strain, anucleate cells were produced. In contrast, overproduction of either MukE or MukB did not cause the defect. In null mutants for the mukF, mukE, and mukB genes, the synchronous initiation of chromosome replication was not affected. The mini-F plasmid was as stably maintained in these mutants as in the wild-type strain. These results indicate that the MukF, MukE, and MukB proteins are involved in the chromosome partitioning steps, but are not required for mini-F plasmid partitioning.
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Affiliation(s)
- K Yamanaka
- Department of Molecular Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University School of Medicine, Japan
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