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Mycobacterium smegmatis does not display functional redundancy in nitrate reductase enzymes. PLoS One 2021; 16:e0245745. [PMID: 33471823 PMCID: PMC7816997 DOI: 10.1371/journal.pone.0245745] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 01/06/2021] [Indexed: 12/04/2022] Open
Abstract
Reduction of nitrate to nitrite in bacteria is an essential step in the nitrogen cycle, catalysed by a variety of nitrate reductase (NR) enzymes. The soil dweller, Mycobacterium smegmatis is able to assimilate nitrate and herein we set out to confirm the genetic basis for this by probing NR activity in mutants defective for putative nitrate reductase (NR) encoding genes. In addition to the annotated narB and narGHJI, bioinformatics identified three other putative NR-encoding genes: MSMEG_4206, MSMEG_2237 and MSMEG_6816. To assess the relative contribution of each, the corresponding gene loci were deleted using two-step allelic replacement, individually and in combination. The resulting strains were tested for their ability to assimilate nitrate and reduce nitrate under aerobic and anaerobic conditions, using nitrate assimilation and modified Griess assays. We demonstrated that narB, narGHJI, MSMEG_2237 and MSMEG_6816 were individually dispensable for nitrate assimilation and for nitrate reductase activity under aerobic and anaerobic conditions. Only deletion of MSMEG_4206 resulted in significant reduction in nitrate assimilation under aerobic conditions. These data confirm that in M. smegmatis, narB, narGHJI, MSMEG_2237 and MSMEG_6816 are not required for nitrate reduction as MSMEG_4206 serves as the sole assimilatory NR.
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Park J, Lee HH, Jung H, Seo YS. Transcriptome analysis to understand the effects of the toxoflavin and tropolone produced by phytopathogenic Burkholderia on Escherichia coli. J Microbiol 2019; 57:781-794. [DOI: 10.1007/s12275-019-9330-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 07/18/2019] [Accepted: 07/25/2019] [Indexed: 12/13/2022]
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O. M. K. BIOTECHNICAL INFORMATION SYSTEMS FOR MONITORING OF CHEMICALS IN ENVIRONMENT: BIOPHYSICAL APPROACH. BIOTECHNOLOGIA ACTA 2019. [DOI: 10.15407/biotech12.01.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Klyuchko OM. ELECTRONIC INFORMATION SYSTEMS FOR MONITORING OF POPULATIONS AND MIGRATIONS OF INSECTS. BIOTECHNOLOGIA ACTA 2018. [DOI: 10.15407/biotech11.05.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Jeong H, Sim YM, Kim HJ, Lee SJ. Unveiling the Hybrid Genome Structure of Escherichia coli RR1 (HB101 RecA +). Front Microbiol 2017; 8:585. [PMID: 28421066 PMCID: PMC5379014 DOI: 10.3389/fmicb.2017.00585] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Accepted: 03/21/2017] [Indexed: 01/26/2023] Open
Abstract
There have been extensive genome sequencing studies for Escherichia coli strains, particularly for pathogenic isolates, because fast determination of pathogenic potential and/or drug resistance and their propagation routes is crucial. For laboratory E. coli strains, however, genome sequence information is limited except for several well-known strains. We determined the complete genome sequence of laboratory E. coli strain RR1 (HB101 RecA+), which has long been used as a general cloning host. A hybrid genome sequence of K-12 MG1655 and B BL21(DE3) was constructed based on the initial mapping of Illumina HiSeq reads to each reference, and iterative rounds of read mapping, variant detection, and consensus extraction were carried out. Finally, PCR and Sanger sequencing-based finishing were applied to resolve non-single nucleotide variant regions with aberrant read depths and breakpoints, most of them resulting from prophages and insertion sequence transpositions that are not present in the reference genome sequence. We found that 96.9% of the RR1 genome is derived from K-12, and identified exact crossover junctions between K-12 and B genomic fragments. However, because RR1 has experienced a series of genetic manipulations since branching from the common ancestor, it has a set of mutations different from those found in K-12 MG1655. As well as identifying all known genotypes of RR1 on the basis of genomic context, we found novel mutations. Our results extend current knowledge of the genotype of RR1 and its relatives, and provide insights into the pedigree, genomic background, and physiology of common laboratory strains.
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Affiliation(s)
- Haeyoung Jeong
- Infectious Disease Research Center, Korea Research Institute of Bioscience and BiotechnologyDaejeon, South Korea.,Biosystems and Bioengineering Program, University of Science and TechnologyDaejeon, South Korea
| | - Young Mi Sim
- Korean Bioinformation Center, Korea Research Institute of Bioscience and BiotechnologyDaejeon, South Korea
| | - Hyun Ju Kim
- Biosystems and Bioengineering Program, University of Science and TechnologyDaejeon, South Korea
| | - Sang Jun Lee
- Department of Systems Biotechnology, Chung-Ang UniversityAnseong, South Korea
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Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP, Zaslavsky L, Lomsadze A, Pruitt KD, Borodovsky M, Ostell J. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 2016; 44:6614-24. [PMID: 27342282 PMCID: PMC5001611 DOI: 10.1093/nar/gkw569] [Citation(s) in RCA: 4892] [Impact Index Per Article: 543.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 06/08/2016] [Accepted: 06/13/2016] [Indexed: 12/01/2022] Open
Abstract
Recent technological advances have opened unprecedented opportunities for large-scale sequencing and analysis of populations of pathogenic species in disease outbreaks, as well as for large-scale diversity studies aimed at expanding our knowledge across the whole domain of prokaryotes. To meet the challenge of timely interpretation of structure, function and meaning of this vast genetic information, a comprehensive approach to automatic genome annotation is critically needed. In collaboration with Georgia Tech, NCBI has developed a new approach to genome annotation that combines alignment based methods with methods of predicting protein-coding and RNA genes and other functional elements directly from sequence. A new gene finding tool, GeneMarkS+, uses the combined evidence of protein and RNA placement by homology as an initial map of annotation to generate and modify ab initio gene predictions across the whole genome. Thus, the new NCBI's Prokaryotic Genome Annotation Pipeline (PGAP) relies more on sequence similarity when confident comparative data are available, while it relies more on statistical predictions in the absence of external evidence. The pipeline provides a framework for generation and analysis of annotation on the full breadth of prokaryotic taxonomy. For additional information on PGAP see https://www.ncbi.nlm.nih.gov/genome/annotation_prok/ and the NCBI Handbook, https://www.ncbi.nlm.nih.gov/books/NBK174280/.
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Affiliation(s)
- Tatiana Tatusova
- National Center for Biotechnology Information, U.S. National Library of Medicine, Bethesda, MD 20894, USA
| | - Michael DiCuccio
- National Center for Biotechnology Information, U.S. National Library of Medicine, Bethesda, MD 20894, USA
| | - Azat Badretdin
- National Center for Biotechnology Information, U.S. National Library of Medicine, Bethesda, MD 20894, USA
| | - Vyacheslav Chetvernin
- National Center for Biotechnology Information, U.S. National Library of Medicine, Bethesda, MD 20894, USA
| | - Eric P Nawrocki
- National Center for Biotechnology Information, U.S. National Library of Medicine, Bethesda, MD 20894, USA
| | - Leonid Zaslavsky
- National Center for Biotechnology Information, U.S. National Library of Medicine, Bethesda, MD 20894, USA
| | - Alexandre Lomsadze
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech, Atlanta, GA 30332, USA
| | - Kim D Pruitt
- National Center for Biotechnology Information, U.S. National Library of Medicine, Bethesda, MD 20894, USA
| | - Mark Borodovsky
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech, Atlanta, GA 30332, USA School of Computational Science and Engineering, Georgia Tech, Atlanta, GA 30332, USA
| | - James Ostell
- National Center for Biotechnology Information, U.S. National Library of Medicine, Bethesda, MD 20894, USA
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Nakahigashi K, Takai Y, Kimura M, Abe N, Nakayashiki T, Shiwa Y, Yoshikawa H, Wanner BL, Ishihama Y, Mori H. Comprehensive identification of translation start sites by tetracycline-inhibited ribosome profiling. DNA Res 2016; 23:193-201. [PMID: 27013550 PMCID: PMC4909307 DOI: 10.1093/dnares/dsw008] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2015] [Accepted: 02/06/2016] [Indexed: 01/12/2023] Open
Abstract
Tetracycline-inhibited ribosome profiling (TetRP) provides a powerful new experimental tool for comprehensive genome-wide identification of translation initiation sites in bacteria. We validated TetRP by confirming the translation start sites of protein-coding genes in accordance with the 2006 version of Escherichia coli K-12 annotation record (GenBank U00096.2) and found ∼150 new start sites within 60 nucleotides of the annotated site. This analysis revealed 72 per cent of the genes whose initiation site annotations were changed from the 2006 GenBank record to the newer 2014 annotation record (GenBank U00096.3), indicating a high sensitivity. Also, results from reporter fusion and proteomics of N-terminally enriched peptides showed high specificity of the TetRP results. In addition, we discovered over 300 translation start sites within non-coding, intergenic regions of the genome, using a threshold that retains ∼2,000 known coding genes. While some appear to correspond to pseudogenes, others may encode small peptides or have previously unforeseen roles. In summary, we showed that ribosome profiling upon translation inhibition by tetracycline offers a simple, reliable and comprehensive experimental tool for precise annotation of translation start sites of expressed genes in bacteria.
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Affiliation(s)
- Kenji Nakahigashi
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0017, Japan
| | - Yuki Takai
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0017, Japan
| | - Michiko Kimura
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Nozomi Abe
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0017, Japan
| | - Toru Nakayashiki
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0101, Japan
| | - Yuh Shiwa
- Genome Research Center, NODAI Research Institute, Tokyo University of Agriculture, Tokyo 156-8502, Japan
| | - Hirofumi Yoshikawa
- Genome Research Center, NODAI Research Institute, Tokyo University of Agriculture, Tokyo 156-8502, Japan Department of Bioscience, Tokyo University of Agriculture, Tokyo 156-8502, Japan
| | - Barry L Wanner
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Yasushi Ishihama
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Hirotada Mori
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0101, Japan
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Chang YL, Li WY, Miao H, Yang SQ, Li R, Wang X, Li WQ, Chen KM. Comprehensive Genomic Analysis and Expression Profiling of the NOX Gene Families under Abiotic Stresses and Hormones in Plants. Genome Biol Evol 2016; 8:791-810. [PMID: 26907500 PMCID: PMC4824067 DOI: 10.1093/gbe/evw035] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Plasma membrane NADPH oxidases (NOXs) are key producers of reactive oxygen species under both normal and stress conditions in plants and they form functional subfamilies. Studies of these subfamilies indicated that they show considerable evolutionary selection. We performed a comparative genomic analysis that identified 50 ferric reduction oxidases (FRO) and 77 NOX gene homologs from 20 species representing the eight major plant lineages within the supergroup Plantae: glaucophytes, rhodophytes, chlorophytes, bryophytes, lycophytes, gymnosperms, monocots, and eudicots. Phylogenetic and structural analysis classified these FRO and NOX genes into four well-conserved groups represented as NOX, FRO I, FRO II, and FRO III. Further analysis of NOXs of phylogenetic and exon/intron structures showed that single intron loss and gain had occurred, yielding the diversified gene structures during the evolution of NOXs family genes and which were classified into four conserved subfamilies which are represented as Sub.I, Sub.II, Sub.III, and Sub.IV. Additionally, both available global microarray data analysis and quantitative real-time PCR experiments revealed that the NOX genes in Arabidopsis and rice (Oryza sativa) have different expression patterns in different developmental stages, various abiotic stresses and hormone treatments. Finally, coexpression network analysis of NOX genes in Arabidopsis and rice revealed that NOXs have significantly correlated expression profiles with genes which are involved in plants metabolic and resistance progresses. All these results suggest that NOX family underscores the functional diversity and divergence in plants. This finding will facilitate further studies of the NOX family and provide valuable information for functional validation of this family in plants.
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Affiliation(s)
- Yan-Li Chang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Wen-Yan Li
- Guangdong Academy of Agricultural Sciences, Argo-Biological Gene Research Center, Guangzhou, Guangdong, P. R. China
| | - Hai Miao
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Shuai-Qi Yang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Ri Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Xiang Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Wen-Qiang Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Kun-Ming Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, P. R. China
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Tatusova T, Ciufo S, Fedorov B, O'Neill K, Tolstoy I. RefSeq microbial genomes database: new representation and annotation strategy. Nucleic Acids Res 2013; 42:D553-9. [PMID: 24316578 PMCID: PMC3965038 DOI: 10.1093/nar/gkt1274] [Citation(s) in RCA: 318] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The source of the microbial genomic sequences in the RefSeq collection is the set of primary sequence records submitted to the International Nucleotide Sequence Database public archives. These can be accessed through the Entrez search and retrieval system at http://www.ncbi.nlm.nih.gov/genome. Next-generation sequencing has enabled researchers to perform genomic sequencing at rates that were unimaginable in the past. Microbial genomes can now be sequenced in a matter of hours, which has led to a significant increase in the number of assembled genomes deposited in the public archives. This huge increase in DNA sequence data presents new challenges for the annotation, analysis and visualization bioinformatics tools. New strategies have been developed for the annotation and representation of reference genomes and sequence variations derived from population studies and clinical outbreaks.
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Affiliation(s)
- Tatiana Tatusova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bldg. 38A 8600 Rockville Pike, Bethesda, MD 20894, USA
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