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Han C, Yu Z, Zhao J, Shi H, Hu J, Yu B, Song J, Shen Y, Xiang W, Wang X. Streptomyces triticagri sp. nov. and Streptomyces triticirhizae sp. nov., two novel Actinobacteria isolated from the rhizosphere soil of wheat ( Triticum aestivum L.). Int J Syst Evol Microbiol 2020; 70:126-138. [PMID: 31613740 DOI: 10.1099/ijsem.0.003727] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Two novel Actinobacteria, designated strains NEAU-YY421T and NEAU-YY642T, were isolated from the rhizosphere soil of wheat (Triticum aestivum L.) collected from Zhumadian, Henan Province, PR China and characterized using a polyphasic approach. Phylogenetic analyses based on 16S rRNA gene sequences showed that strains NEAU-YY421T and NEAU-YY642T belonged to the genus Streptomyces and strain NEAU-YY421T was most closely related to Streptomyces fumanus CGMCC 4.1732T (97.9 % sequence similarity) and Streptomyces naganishii DSM 40282T (97.8 %), and that of strain NEAU-YY642T to Streptomyces zhaozhouensis LZS-5T (98.0 %) and Streptomyces sedi YIM 65188T (97.5 %). The cell walls of the two strains contained ll-diaminopimelic acid as the diagnostic diamino acid and the whole-cell hydrolysates were glucose and ribose. Multilocus sequence analysis using the concatenated sequences of the atp D, gyr B, rec A, rpo B and trp B genes showed that the two strains formed separate branches in the genus Streptomyces. Moreover, a combination of DNA-DNA hybridization results and cultural and physiological properties indicated that the two strains can be distinguished from their closest phylogenetic relatives. Therefore, strains NEAU-YY421T and NEAU-YY642T belong to two novel species in the genus Streptomyces, for which the names Streptomyces triticagri sp. nov. (NEAU-YY421T=CGMCC 4.7476T=DSM 106775T) and Streptomyces triticirhizae sp. nov. (NEAU-YY642T=CCTCC AA 2018092T=DSM 107172T) are proposed, respectively.
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Affiliation(s)
- Chuanyu Han
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
| | - Zhiyin Yu
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
| | - Junwei Zhao
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
| | - Haoran Shi
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
| | - Jiangmeihui Hu
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
| | - Bing Yu
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
| | - Jia Song
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
| | - Yue Shen
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
| | - Wensheng Xiang
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China.,State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, PR China
| | - Xiangjing Wang
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
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Gupta RS, Patel S. Robust Demarcation of the Family Caryophanaceae ( Planococcaceae) and Its Different Genera Including Three Novel Genera Based on Phylogenomics and Highly Specific Molecular Signatures. Front Microbiol 2020; 10:2821. [PMID: 32010063 PMCID: PMC6971209 DOI: 10.3389/fmicb.2019.02821] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 11/20/2019] [Indexed: 12/12/2022] Open
Abstract
The family Caryophanaceae/Planococcaceae is a taxonomically heterogeneous assemblage of >100 species classified within 13 genera, many of which are polyphyletic. Exhibiting considerable phylogenetic overlap with other families, primarily Bacillaceae, the evolutionary history of this family, containing the potent mosquitocidal species Lysinibacillus sphaericus, remains incoherent. To develop a reliable phylogenetic and taxonomic framework for the family Caryophanaceae/Planococcaceae and its genera, we report comprehensive phylogenetic and comparative genomic analyses on 124 genome sequences from all available Caryophanaceae/Planococcaceae and representative Bacillaceae species. Phylogenetic trees were constructed based on multiple datasets of proteins including 819 core proteins for this group and 87 conserved Firmicutes proteins. Using the core proteins, pairwise average amino acid identity was also determined. In parallel, comparative analyses on protein sequences from these species have identified 92 unique molecular markers (synapomorphies) consisting of conserved signature indels that are specifically shared by either the entire family Caryophanaceae/Planococcaceae or different monophyletic clades present within this family, enabling their reliable demarcation in molecular terms. Based on multiple lines of investigations, 18 monophyletic clades can be reliably distinguished within the family Caryophanaceae/Planococcaceae based on their phylogenetic affinities and identified molecular signatures. Some of these clades are comprised of species from several polyphyletic genera within this family as well as other families. Based on our results, we are proposing the creation of three novel genera within the family Caryophanaceae/Planococcaceae, namely Metalysinibacillus gen. nov., Metasolibacillus gen. nov., and Metaplanococcus gen. nov., as well as the transfer of 25 misclassified species from the families Caryophanaceae/Planococcaceae and Bacillaceae into these three genera and in Planococcus, Solibacillus, Sporosarcina, and Ureibacillus genera. These amendments establish a coherent taxonomy and evolutionary history for the family Caryophanaceae/Planococcaceae, and the described molecular markers provide novel means for diagnostic, genetic, and biochemical studies. Lastly, we are also proposing a consolidation of the family Planococcaceae within the emended family Caryophanaceae.
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Affiliation(s)
- Radhey S Gupta
- Department of Biochemistry and Biomedical Sciences, Faculty of Health Sciences, McMaster University, Hamilton, ON, Canada
| | - Sudip Patel
- Department of Biochemistry and Biomedical Sciences, Faculty of Health Sciences, McMaster University, Hamilton, ON, Canada
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Salwan R, Sharma V. Molecular and biotechnological aspects of secondary metabolites in actinobacteria. Microbiol Res 2020; 231:126374. [DOI: 10.1016/j.micres.2019.126374] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Revised: 11/10/2019] [Accepted: 11/11/2019] [Indexed: 12/21/2022]
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Succession of Microbial Decomposers Is Determined by Litter Type, but Site Conditions Drive Decomposition Rates. Appl Environ Microbiol 2019; 85:AEM.01760-19. [PMID: 31604765 DOI: 10.1128/aem.01760-19] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 10/03/2019] [Indexed: 12/31/2022] Open
Abstract
Soil microorganisms are diverse, although they share functions during the decomposition of organic matter. Thus, preferences for soil conditions and litter quality were explored to understand their niche partitioning. A 1-year-long litterbag transplant experiment evaluated how soil physicochemical traits of contrasting sites combined with chemically distinct litters of sedge (S), milkvetch (M) from a grassland, and beech (B) from forest site decomposition. Litter was assessed by mass loss; C, N, and P contents; and low-molecular-weight compounds. Decomposition was described by the succession of fungi, Actinobacteria, Alphaproteobacteria, and Firmicutes; bacterial diversity; and extracellular enzyme activities. The M litter decomposed faster at the nutrient-poor forest site, where the extracellular enzymes were more active, but microbial decomposers were not more abundant. Actinobacteria abundance was affected by site, while Firmicutes and fungi by litter type and Alphaproteobacteria by both factors. Actinobacteria were characterized as late-stage substrate generalists, while fungi were recognized as substrate specialists and site generalists, particularly in the grassland. Overall, soil conditions determined the decomposition rates in the grassland and forest, but successional patterns of the main decomposers (fungi and Actinobacteria) were determined by litter type. These results suggest that shifts in vegetation mostly affect microbial decomposer community composition.IMPORTANCE Anthropogenic disturbance may cause shifts in vegetation and alter the litter input. We studied the decomposition of different litter types under soil conditions of a nutrient-rich grassland and nutrient-poor forest to identify factors responsible for changes in the community structure and succession of microbial decomposers. This will help to predict the consequences of induced changes on the abundance and activity of microbial decomposers and recognize if the decomposition process and resulting quality and quantity of soil organic matter will be affected at various sites.
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Oberhofer M, Hess J, Leutgeb M, Gössnitzer F, Rattei T, Wawrosch C, Zotchev SB. Exploring Actinobacteria Associated With Rhizosphere and Endosphere of the Native Alpine Medicinal Plant Leontopodium nivale Subspecies alpinum. Front Microbiol 2019; 10:2531. [PMID: 31781058 PMCID: PMC6857621 DOI: 10.3389/fmicb.2019.02531] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 10/21/2019] [Indexed: 11/24/2022] Open
Abstract
The rhizosphere of plants is enriched in nutrients facilitating growth of microorganisms, some of which are recruited as endophytes. Endophytes, especially Actinobacteria, are known to produce a plethora of bioactive compounds. We hypothesized that Leontopodium nivale subsp. alpinum (Edelweiss), a rare alpine medicinal plant, may serve as yet untapped source for uncommon Actinobacteria associated with this plant. Rhizosphere soil of native Alpine plants was used, after physical and chemical pre-treatments, for isolating Actinobacteria. Isolates were selected based on morphology and identified by 16S rRNA gene-based barcoding. Resulting 77 Actinobacteria isolates represented the genera Actinokineospora, Kitasatospora, Asanoa, Microbacterium, Micromonospora, Micrococcus, Mycobacterium, Nocardia, and Streptomyces. In parallel, Edelweiss plants from the same location were surface-sterilized, separated into leaves, roots, rhizomes, and inflorescence and pooled within tissues before genomic DNA extraction. Metagenomic 16S rRNA gene amplicons confirmed large numbers of actinobacterial operational taxonomic units (OTUs) descending in diversity from roots to rhizomes, leaves and inflorescences. These metagenomic data, when queried with isolate sequences, revealed an overlap between the two datasets, suggesting recruitment of soil bacteria by the plant. Moreover, this study uncovered a profound diversity of uncultured Actinobacteria from Rubrobacteridae, Thermoleophilales, Acidimicrobiales and unclassified Actinobacteria specifically in belowground tissues, which may be exploited by a targeted isolation approach in the future.
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Affiliation(s)
- Martina Oberhofer
- Pharmaceutical Biotechnology, Department of Pharmacognosy, University of Vienna, Vienna, Austria
| | - Jaqueline Hess
- Division of Systematic and Evolutionary Botany, Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Marlene Leutgeb
- Pharmaceutical Biotechnology, Department of Pharmacognosy, University of Vienna, Vienna, Austria
| | - Florian Gössnitzer
- Pharmaceutical Biotechnology, Department of Pharmacognosy, University of Vienna, Vienna, Austria
| | - Thomas Rattei
- Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Christoph Wawrosch
- Pharmaceutical Biotechnology, Department of Pharmacognosy, University of Vienna, Vienna, Austria
| | - Sergey B. Zotchev
- Pharmaceutical Biotechnology, Department of Pharmacognosy, University of Vienna, Vienna, Austria
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Li C, Cao P, Jiang M, Sun T, Shen Y, Xiang W, Zhao J, Wang X. Streptomyces oryziradicis sp. nov., a novel actinomycete isolated from rhizosphere soil of rice ( Oryza sativa L.). Int J Syst Evol Microbiol 2019; 70:465-472. [PMID: 31639072 DOI: 10.1099/ijsem.0.003777] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel actinobacterium, designated strain NEAU-C40T, was isolated from the rhizosphere soil of rice (Oryza sativa L.) collected from Northeast Agricultural University in Harbin, Heilongjiang province, north-east PR China, and was characterized using a polyphasic approach. On the basis of results of 16S rRNA gene sequence analysis, strain NEAU-C40T belongs to the genus Streptomyces, and shares highest sequence similarities with Streptomyces polygonati CGMCC 4.7237T (97.9%) and Streptomyces abietis DSM 42080T (97.9%). Morphological and chemotaxonomic characteristics of the strain also supported its assignment to the genus Streptomyces. Cell walls contained ll-diaminopimelic acid and the whole-cell hydrolysates were glucose, rhamnose and ribose. The major menaquinones were identified as MK-9(H8) and MK-9(H6). The major fatty acids were iso-C16:0, anteiso-C15:0, C16:0 and anteiso-C17:0. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol mannoside and an unidentified lipid. The genomic DNA G+C content of strain NEAU-C40T was 71.8 mol%. Moreover, multilocus sequence analysis based on five other housekeeping genes (atp D, gyr B, rpo B, rec A and trp B) and the low level of DNA-DNA relatedness allowed the isolate to be differentiated from its most closely related strains. On the basis of phenotypic, genotypic and phylogenetic data, strain NEAU-C40T can be characterized to represent a novel species of the genus Streptomyces, for which the name Streptomyces oryziradicis sp. nov. is proposed. The type strain is NEAU-C40T (=DSM 107943T=CCTCC AA 2018038T).
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Affiliation(s)
- Chenxu Li
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, PR China
| | - Peng Cao
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, PR China
| | - Mengqi Jiang
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, PR China
| | - Tianyu Sun
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, PR China
| | - Yue Shen
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, PR China
| | - Wensheng Xiang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, PR China.,Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, PR China
| | - Junwei Zhao
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, PR China
| | - Xiangjing Wang
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, PR China
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Musiol-Kroll EM, Tocchetti A, Sosio M, Stegmann E. Challenges and advances in genetic manipulation of filamentous actinomycetes - the remarkable producers of specialized metabolites. Nat Prod Rep 2019; 36:1351-1369. [PMID: 31517370 DOI: 10.1039/c9np00029a] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Covering: up to February 2019Actinomycetes are Gram positive bacteria of the phylum Actinobacteria. These organisms are one of the most important sources of structurally diverse, clinically used antibiotics and other valuable bioactive products, as well as biotechnologically relevant enzymes. Most strains were discovered by their ability to produce a given molecule and were often poorly characterized, physiologically and genetically. The development of genetic methods for Streptomyces and related filamentous actinomycetes has led to the successful manipulation of antibiotic biosynthesis to attain structural modification of microbial metabolites that would have been inaccessible by chemical means and improved production yields. Moreover, genome mining reveals that actinomycete genomes contain multiple biosynthetic gene clusters (BGCs), however only a few of them are expressed under standard laboratory conditions, leading to the production of the respective compound(s). Thus, to access and activate the so-called "silent" BGCs, to improve their biosynthetic potential and to discover novel natural products methodologies for genetic manipulation are required. Although different methods have been applied for many actinomycete strains, genetic engineering is still remaining very challenging for some "underexplored" and poorly characterized actinomycetes. This review summarizes the strategies developed to overcome the obstacles to genetic manipulation of actinomycetes and allowing thereby rational genetic engineering of this industrially relevant group of microorganisms. At the end of this review we give some tips to researchers with limited or no previous experience in genetic manipulation of actinomycetes. The article covers the most relevant literature published until February 2019.
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Affiliation(s)
- Ewa M Musiol-Kroll
- University of Tübingen, Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Microbiology/Biotechnology, Auf der Morgenstelle 28, Tübingen, 72076, Germany.
| | | | | | - Evi Stegmann
- University of Tübingen, Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Microbiology/Biotechnology, Auf der Morgenstelle 28, Tübingen, 72076, Germany.
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New genus-specific primers for PCR identification of Rubrobacter strains. Antonie Van Leeuwenhoek 2019; 112:1863-1874. [PMID: 31407134 PMCID: PMC6834744 DOI: 10.1007/s10482-019-01314-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 08/01/2019] [Indexed: 12/02/2022]
Abstract
A set of oligonucleotide primers, Rubro223f and Rubro454r, were found to amplify a 267 nucleotide sequence of 16S rRNA genes of Rubrobacter type strains. The primers distinguished members of this genus from other deeply-rooted actinobacterial lineages corresponding to the genera Conexibacter, Gaiella, Parviterribacter, Patulibacter, Solirubrobacter and Thermoleophilum of the class Thermoleophilia. Amplification of DNA bands of about 267 nucleotides were generated from environmental DNA extracted from soil samples taken from two locations in the Atacama Desert. Sequencing of a DNA library prepared from the bands showed that all of the clones fell within the evolutionary radiation occupied by the genus Rubrobacter. Most of the clones were assigned to two lineages that were well separated from phyletic lines composed of Rubrobacter type strains. It can be concluded that primers Rubro223f and Rubro454r are specific for the genus Rubrobacter and can be used to detect the presence and abundance of members of this genus in the Atacama Desert and other biomes.
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Kamariah N, Huber RG, Nartey W, Bhushan S, Bond PJ, Grüber G. Structure and subunit arrangement of Mycobacterial F1FO ATP synthase and novel features of the unique mycobacterial subunit δ. J Struct Biol 2019; 207:199-208. [DOI: 10.1016/j.jsb.2019.05.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 05/21/2019] [Accepted: 05/23/2019] [Indexed: 02/08/2023]
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Hu D, Zang Y, Mao Y, Gao B. Identification of Molecular Markers That Are Specific to the Class Thermoleophilia. Front Microbiol 2019; 10:1185. [PMID: 31178855 PMCID: PMC6544083 DOI: 10.3389/fmicb.2019.01185] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 05/09/2019] [Indexed: 12/26/2022] Open
Abstract
The class Thermoleophilia is one of the deep-rooting lineages within the Actinobacteria phylum and metagenomic investigation of microbial diversity suggested that species associated with the class Thermoleophilia are abundant in hot spring and soil samples. However, very few species of this class have been cultivated and characterized. Our understanding of the phylogeny and taxonomy of Thermoleophilia is solely based on 16S rRNA sequence analysis of limited cultivable representatives, but no other phenotypic or genotypic characteristics are known that can clearly discriminate members of this class from the other taxonomic units within the kingdom bacteria. This study reports phylogenomic analysis for 12 sequenced members of this class and clearly resolves the interrelationship of not yet cultivated species with reconstructed genomes and known type species. Comparative genome analysis discovered 12 CSIs in different proteins and 32 CSPs that are specific to all species of this class. In addition, a large number of CSIs or CSPs were identified to be unique to certain lineages within this class. This study represents the first and most comprehensive phylogenetic analysis of the class Thermoleophilia, and the identified CSIs and CSPs provide valuable molecular markers for the identification and delineation of species belonging to this class or its subordinate taxa.
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Affiliation(s)
- Danyu Hu
- CAS Key Laboratory of Tropical Marine Bio Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yang Zang
- CAS Key Laboratory of Tropical Marine Bio Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yingjin Mao
- CAS Key Laboratory of Tropical Marine Bio Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Beile Gao
- CAS Key Laboratory of Tropical Marine Bio Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
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61
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Khadka B, Gupta RS. Novel Molecular Signatures in the PIP4K/PIP5K Family of Proteins Specific for Different Isozymes and Subfamilies Provide Important Insights into the Evolutionary Divergence of this Protein Family. Genes (Basel) 2019; 10:genes10040312. [PMID: 31010098 PMCID: PMC6523245 DOI: 10.3390/genes10040312] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 04/10/2019] [Accepted: 04/15/2019] [Indexed: 02/07/2023] Open
Abstract
Members of the PIP4K/PIP5K family of proteins, which generate the highly important secondary messenger phosphatidylinositol-4,5-bisphosphate, play central roles in regulating diverse signaling pathways. In eukaryotic organisms, multiple isozymes and subfamilies of PIP4K/PIP5K proteins are found and it is of much interest to understand their evolution and species distribution and what unique molecular and biochemical characteristics distinguish specific isozymes and subfamilies of proteins. We report here the species distribution of different PIP4K/PIP5K family of proteins in eukaryotic organisms and phylogenetic analysis based on their protein sequences. Our results indicate that the distinct homologs of both PIP4K and PIP5K are found in different organisms belonging to the Holozoa clade of eukaryotes, which comprises of various metazoan phyla as well as their close unicellular relatives Choanoflagellates and Filasterea. In contrast, the deeper-branching eukaryotic lineages, as well as plants and fungi, contain only a single homolog of the PIP4K/PIP5K proteins. In parallel, our comparative analyses of PIP4K/PIP5K protein sequences have identified six highly-specific molecular markers consisting of conserved signature indels (CSIs) that are uniquely shared by either the PIP4K or PIP5K proteins, or both, or specific subfamilies of these proteins. Of these molecular markers, 2 CSIs are distinctive characteristics of all PIP4K homologs, 1 CSI distinguishes the PIP4K and PIP5K homologs from the Holozoa clade of species from the ancestral form of PIP4K/PIP5K found in deeper-branching eukaryotic lineages. The remaining three CSIs are specific for the PIP5Kα, PIP5Kβ, and PIP4Kγ subfamilies of proteins from vertebrate species. These molecular markers provide important means for distinguishing different PIP4K/PIP5K isozymes as well as some of their subfamilies. In addition, the distribution patterns of these markers in different isozymes provide important insights into the evolutionary divergence of PIP4K/PIP5K proteins. Our results support the view that the Holozoa clade of eukaryotic organisms shared a common ancestor exclusive of the other eukaryotic lineages and that the initial gene duplication event leading to the divergence of distinct types of PIP4K and PIP5K homologs occurred in a common ancestor of this clade. Based on the results gleaned from different studies presented here, a model for the evolutionary divergence of the PIP4K/PIP5K family of proteins is presented.
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Affiliation(s)
- Bijendra Khadka
- Department of Biochemistry and Biomedical Sciences McMaster University, Hamilton, ON L8N 3Z5, Canada.
| | - Radhey S Gupta
- Department of Biochemistry and Biomedical Sciences McMaster University, Hamilton, ON L8N 3Z5, Canada.
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62
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Tischler D, van Berkel WJH, Fraaije MW. Editorial: Actinobacteria, a Source of Biocatalytic Tools. Front Microbiol 2019; 10:800. [PMID: 31040839 PMCID: PMC6477052 DOI: 10.3389/fmicb.2019.00800] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 03/28/2019] [Indexed: 11/28/2022] Open
Affiliation(s)
- Dirk Tischler
- Microbial Biotechnology, Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Willem J H van Berkel
- Laboratory of Biochemistry, Wageningen University & Research, Wageningen, Netherlands
| | - Marco W Fraaije
- Molecular Enzymology, University of Groningen, Groningen, Netherlands
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63
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Sevigny JL, Rothenheber D, Diaz KS, Zhang Y, Agustsson K, Bergeron RD, Thomas WK. Marker genes as predictors of shared genomic function. BMC Genomics 2019; 20:268. [PMID: 30947688 PMCID: PMC6449922 DOI: 10.1186/s12864-019-5641-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 03/24/2019] [Indexed: 12/15/2022] Open
Abstract
Background Although high-throughput marker gene studies provide valuable insight into the diversity and relative abundance of taxa in microbial communities, they do not provide direct measures of their functional capacity. Recently, scientists have shown a general desire to predict functional profiles of microbial communities based on phylogenetic identification inferred from marker genes, and recent tools have been developed to link the two. However, to date, no large-scale examination has quantified the correlation between the marker gene based taxonomic identity and protein coding gene conservation. Here we utilize 4872 representative prokaryotic genomes from NCBI to investigate the relationship between marker gene identity and shared protein coding gene content. Results Even at 99–100% marker gene identity, genomes share on average less than 75% of their protein coding gene content. This occurs regardless of the marker gene(s) used: V4 region of the 16S rRNA, complete 16S rRNA, or single copy orthologs through a multi-locus sequence analysis. An important aspect related to this observation is the intra-organism variation of 16S copies from a single genome. Although the majority of 16S copies were found to have high sequence similarity (> 99%), several genomes contained copies that were highly diverged (< 97% identity). Conclusions This is the largest comparison between marker gene similarity and shared protein coding gene content to date. The study highlights the limitations of inferring a microbial community’s functions based on marker gene phylogeny. The data presented expands upon the results of previous studies that examined one or few bacterial species and supports the hypothesis that 16S rRNA and other marker genes cannot be directly used to fully predict the functional potential of a bacterial community. Electronic supplementary material The online version of this article (10.1186/s12864-019-5641-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Joseph L Sevigny
- Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, 46 College Rd, Rudman Hall, Durham, NH, 03824, USA. .,Hubbard Center for Genome Studies, University of New Hampshire, 35 Colovos Rd, Gregg Hall, Durham, NH, 03824, USA.
| | - Derek Rothenheber
- Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, 46 College Rd, Rudman Hall, Durham, NH, 03824, USA
| | - Krystalle Sharlyn Diaz
- Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, 46 College Rd, Rudman Hall, Durham, NH, 03824, USA.,Hubbard Center for Genome Studies, University of New Hampshire, 35 Colovos Rd, Gregg Hall, Durham, NH, 03824, USA
| | - Ying Zhang
- Department of Computer Science, University of New Hampshire, 33 Academic Way, Kingsbury Hall, Durham, NH, 0324, USA
| | - Kristin Agustsson
- Department of Computer Science, University of New Hampshire, 33 Academic Way, Kingsbury Hall, Durham, NH, 0324, USA
| | - R Daniel Bergeron
- Department of Computer Science, University of New Hampshire, 33 Academic Way, Kingsbury Hall, Durham, NH, 0324, USA
| | - W Kelley Thomas
- Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, 46 College Rd, Rudman Hall, Durham, NH, 03824, USA.,Hubbard Center for Genome Studies, University of New Hampshire, 35 Colovos Rd, Gregg Hall, Durham, NH, 03824, USA
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64
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Streptomyces inhibens sp. nov., a novel actinomycete isolated from rhizosphere soil of wheat (Triticum aestivum L.). Int J Syst Evol Microbiol 2019; 69:688-695. [DOI: 10.1099/ijsem.0.003204] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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65
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Gupta RS. Commentary: Genome-Based Taxonomic Classification of the Phylum Actinobacteria. Front Microbiol 2019; 10:206. [PMID: 30853945 PMCID: PMC6395429 DOI: 10.3389/fmicb.2019.00206] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 01/24/2019] [Indexed: 11/20/2022] Open
Affiliation(s)
- Radhey S. Gupta
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
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66
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Secondary Metabolites of Endophytic Actinomycetes: Isolation, Synthesis, Biosynthesis, and Biological Activities. PROGRESS IN THE CHEMISTRY OF ORGANIC NATURAL PRODUCTS 108 2019; 108:207-296. [DOI: 10.1007/978-3-030-01099-7_3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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67
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Abstract
Actinobacteria is a group of diverse bacteria. Most species in this class of bacteria are filamentous aerobes found in soil, including the genus Streptomyces perhaps best known for their fascinating capabilities of producing antibiotics. These bacteria typically have a Gram-positive cell envelope, comprised of a plasma membrane and a thick peptidoglycan layer. However, there is a notable exception of the Corynebacteriales order, which has evolved a unique type of outer membrane likely as a consequence of convergent evolution. In this chapter, we will focus on the unique cell envelope of this order. This cell envelope features the peptidoglycan layer that is covalently modified by an additional layer of arabinogalactan . Furthermore, the arabinogalactan layer provides the platform for the covalent attachment of mycolic acids , some of the longest natural fatty acids that can contain ~100 carbon atoms per molecule. Mycolic acids are thought to be the main component of the outer membrane, which is composed of many additional lipids including trehalose dimycolate, also known as the cord factor. Importantly, a subset of bacteria in the Corynebacteriales order are pathogens of human and domestic animals, including Mycobacterium tuberculosis. The surface coat of these pathogens are the first point of contact with the host immune system, and we now know a number of host receptors specific to molecular patterns exposed on the pathogen's surface, highlighting the importance of understanding how the cell envelope of Actinobacteria is structured and constructed. This chapter describes the main structural and biosynthetic features of major components found in the actinobacterial cell envelopes and highlights the key differences between them.
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Affiliation(s)
- Kathryn C Rahlwes
- Department of Microbiology, University of Massachusetts, 639 North Pleasant Street, Amherst, MA, 01003, USA
| | - Ian L Sparks
- Department of Microbiology, University of Massachusetts, 639 North Pleasant Street, Amherst, MA, 01003, USA
| | - Yasu S Morita
- Department of Microbiology, University of Massachusetts, 639 North Pleasant Street, Amherst, MA, 01003, USA.
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68
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Isolation and characterization of bacteriophage NTR1 infectious for Nocardia transvalensis and other Nocardia species. Virus Genes 2018; 55:257-265. [DOI: 10.1007/s11262-018-1625-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 12/11/2018] [Indexed: 10/27/2022]
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69
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Robust demarcation of fourteen different species groups within the genus Streptococcus based on genome-based phylogenies and molecular signatures. INFECTION GENETICS AND EVOLUTION 2018; 66:130-151. [DOI: 10.1016/j.meegid.2018.09.020] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 09/12/2018] [Accepted: 09/19/2018] [Indexed: 11/21/2022]
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70
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A phylogenomic and molecular markers based taxonomic framework for members of the order Entomoplasmatales: proposal for an emended order Mycoplasmatales containing the family Spiroplasmataceae and emended family Mycoplasmataceae comprised of six genera. Antonie van Leeuwenhoek 2018; 112:561-588. [PMID: 30392177 DOI: 10.1007/s10482-018-1188-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 10/14/2018] [Indexed: 01/01/2023]
Abstract
The "Spiroplasma cluster" is a taxonomically heterogeneous assemblage within the phylum Tenericutes encompassing different Entomoplasmatales species as well as the genus Mycoplasma, type genus of the order Mycoplasmatales. Within this cluster, the family Entomoplasmataceae contains two non-cohesive genera Entomoplasma and Mesoplasma with their members exhibiting extensive polyphyletic branching; additionally, the genus Mycoplasma is also embedded within this family. Genome sequences are now available for all 19 Entomoplasmataceae species with validly published names, as well as 6 of the 7 species from the genus Mycoplasma. With the aim of developing a reliable phylogenetic and taxonomic framework for the family Entomoplasmataceae, exhaustive phylogenetic and comparative genomic studies were carried out on these genome sequences. Phylogenetic trees were constructed based on concatenated sequences of 121 core proteins for this cluster, 67 conserved proteins shared with the phylum Firmicutes, 40 ribosomal proteins, three major subunits of RNA polymerase (RpoA, B and C) by different means and also for the 16S rRNA gene sequences. The interspecies relationships as well as different species groups observed in these trees were identical and robustly resolved. In all of these trees, members of the genera Mesoplasma and Entomoplasma formed three and two distinct clades, respectively, which were interspersed among the members of the other genus. The observed species groupings in the phylogenetic trees are independently strongly supported by our identification of 103 novel molecular markers or synapomorphies in the forms of conserved signature indels and conserved signature proteins, which are uniquely shared by the members of different observed species clades. To account for the different observed species clades, we are proposing a division of the genus Mesoplasma into an emended genus Mesoplasma and two new genera Tullyiplasma gen. nov. and Edwardiiplasma gen. nov. Likewise, to recognize the distinct species groupings of Entomoplasma, we are proposing its division into an emended genus Entomoplasma and a new genus Williamsoniiplasma gen. nov. Lastly, to rectify the long-existing taxonomic anomaly caused by the presence of genus Mycoplasma (order Mycoplasmatales) within the Entomoplasmatales, we are proposing an emendation of the family Mycoplasmataceae to include both Entomoplasmataceae plus Mycoplasma species and an emendation of the order Mycoplasmatales, which now comprises of the emended family Mycoplasmataceae and the family Spiroplasmataceae. The taxonomic reclassifications proposed here accurately reflect the species relationships within this group of Tenericutes and they should lead to a better understanding of their biological and pathogenic characteristics.
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71
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Gupta RS. Impact of Genomics on Clarifying the Evolutionary Relationships amongst Mycobacteria: Identification of Molecular Signatures Specific for the Tuberculosis-Complex of Bacteria with Potential Applications for Novel Diagnostics and Therapeutics. High Throughput 2018; 7:ht7040031. [PMID: 30279355 PMCID: PMC6306742 DOI: 10.3390/ht7040031] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 09/25/2018] [Accepted: 09/27/2018] [Indexed: 12/31/2022] Open
Abstract
An alarming increase in tuberculosis (TB) caused by drug-resistant strains of Mycobacterium tuberculosis has created an urgent need for new antituberculosis drugs acting via novel mechanisms. Phylogenomic and comparative genomic analyses reviewed here reveal that the TB causing bacteria comprise a small group of organisms differing from all other mycobacteria in numerous regards. Comprehensive analyses of protein sequences from mycobacterial genomes have identified 63 conserved signature inserts and deletions (indels) (CSIs) in important proteins that are distinctive characteristics of the TB-complex of bacteria. The identified CSIs provide potential means for development of novel diagnostics as well as therapeutics for the TB-complex of bacteria based on four key observations: (i) The CSIs exhibit a high degree of exclusivity towards the TB-complex of bacteria; (ii) Earlier work on CSIs provide evidence that they play important/essential functions in the organisms for which they exhibit specificity; (iii) CSIs are located in surface-exposed loops of the proteins implicated in mediating novel interactions; (iv) Homologs of the CSIs containing proteins, or the CSIs in such homologs, are generally not found in humans. Based on these characteristics, it is hypothesized that the high-throughput virtual screening for compounds binding specifically to the CSIs (or CSI containing regions) and thereby inhibiting the cellular functions of the CSIs could lead to the discovery of a novel class of drugs specifically targeting the TB-complex of organisms.
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Affiliation(s)
- Radhey S Gupta
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8N 3Z5, Canada.
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72
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Benndorf R, Guo H, Sommerwerk E, Weigel C, Garcia-Altares M, Martin K, Hu H, Küfner M, de Beer ZW, Poulsen M, Beemelmanns C. Natural Products from Actinobacteria Associated with Fungus-Growing Termites. Antibiotics (Basel) 2018; 7:E83. [PMID: 30217010 PMCID: PMC6165096 DOI: 10.3390/antibiotics7030083] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 09/02/2018] [Accepted: 09/03/2018] [Indexed: 12/03/2022] Open
Abstract
The chemical analysis of insect-associated Actinobacteria has attracted the interest of natural product chemists in the past years as bacterial-produced metabolites are sought to be crucial for sustaining and protecting the insect host. The objective of our study was to evaluate the phylogeny and bioprospecting of Actinobacteria associated with fungus-growing termites. We characterized 97 Actinobacteria from the gut, exoskeleton, and fungus garden (comb) of the fungus-growing termite Macrotermes natalensis and used two different bioassays to assess their general antimicrobial activity. We selected two strains for chemical analysis and investigated the culture broth of the axenic strains and fungus-actinobacterium co-cultures. From these studies, we identified the previously-reported PKS-derived barceloneic acid A and the PKS-derived rubterolones. Analysis of culture broth yielded a new dichlorinated diketopiperazine derivative and two new tetracyclic lanthipeptides, named rubrominins A and B. The discussed natural products highlight that insect-associated Actinobacteria are highly prolific natural product producers yielding important chemical scaffolds urgently needed for future drug development programs.
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Affiliation(s)
- René Benndorf
- Leibniz Institute for Natural Product Research and Infection Biology-Hans-Knöll-Institute, Beutenbergstraße 11a, 07745 Jena, Germany.
| | - Huijuan Guo
- Leibniz Institute for Natural Product Research and Infection Biology-Hans-Knöll-Institute, Beutenbergstraße 11a, 07745 Jena, Germany.
| | - Elisabeth Sommerwerk
- Leibniz Institute for Natural Product Research and Infection Biology-Hans-Knöll-Institute, Beutenbergstraße 11a, 07745 Jena, Germany.
| | - Christiane Weigel
- Leibniz Institute for Natural Product Research and Infection Biology-Hans-Knöll-Institute, Beutenbergstraße 11a, 07745 Jena, Germany.
| | - Maria Garcia-Altares
- Leibniz Institute for Natural Product Research and Infection Biology-Hans-Knöll-Institute, Beutenbergstraße 11a, 07745 Jena, Germany.
| | - Karin Martin
- Leibniz Institute for Natural Product Research and Infection Biology-Hans-Knöll-Institute, Beutenbergstraße 11a, 07745 Jena, Germany.
| | - Haofu Hu
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, 2100 Copenhagen East, Denmark.
| | - Michelle Küfner
- Leibniz Institute for Natural Product Research and Infection Biology-Hans-Knöll-Institute, Beutenbergstraße 11a, 07745 Jena, Germany.
| | - Z Wilhelm de Beer
- Department of Microbiology and Plant Pathology, Forestry and Agriculture Biotechnology Institute, University of Pretoria, Pretoria 0001, South Africa.
| | - Michael Poulsen
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, 2100 Copenhagen East, Denmark.
| | - Christine Beemelmanns
- Leibniz Institute for Natural Product Research and Infection Biology-Hans-Knöll-Institute, Beutenbergstraße 11a, 07745 Jena, Germany.
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73
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Morosov X, Davoudi CF, Baumgart M, Brocker M, Bott M. The copper-deprivation stimulon of Corynebacterium glutamicum comprises proteins for biogenesis of the actinobacterial cytochrome bc 1- aa 3 supercomplex. J Biol Chem 2018; 293:15628-15640. [PMID: 30154248 DOI: 10.1074/jbc.ra118.004117] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 08/21/2018] [Indexed: 01/01/2023] Open
Abstract
Aerobic respiration in Corynebacterium glutamicum involves a cytochrome bc 1-aa 3 supercomplex with a diheme cytochrome c 1, which is the only c-type cytochrome in this species. This organization is considered as typical for aerobic Actinobacteria. Whereas the biogenesis of heme-copper type oxidases like cytochrome aa 3 has been studied extensively in α-proteobacteria, yeast, and mammals, nothing is known about this process in Actinobacteria. Here, we searched for assembly proteins of the supercomplex by identifying the copper-deprivation stimulon, which might include proteins that insert copper into cytochrome aa 3 Using gene expression profiling, we found two copper starvation-induced proteins for supercomplex formation. The Cg2699 protein, named CtiP, contained 16 predicted transmembrane helices, and its sequence was similar to that of the copper importer CopD of Pseudomonas syringae in the N-terminal half and to the cytochrome oxidase maturation protein CtaG of Bacillus subtilis in its C-terminal half. CtiP deletion caused a growth defect similar to that produced by deletion of subunit I of cytochrome aa 3, increased copper tolerance, triggered expression of the copper-deprivation stimulon under copper sufficiency, and prevented co-purification of the supercomplex subunits. The secreted Cg1884 protein, named CopC, had a C-terminal transmembrane helix and contained a Cu(II)-binding motif. Its absence caused a conditional growth defect, increased copper tolerance, and also prevented co-purification of the supercomplex subunits. CtiP and CopC are conserved among aerobic Actinobacteria, and we propose a model of their functions in cytochrome aa 3 biogenesis. Furthermore, we found that the copper-deprivation response involves additional regulators besides the ECF sigma factor SigC.
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Affiliation(s)
- Xenia Morosov
- From the Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Cedric-Farhad Davoudi
- From the Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Meike Baumgart
- From the Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Melanie Brocker
- From the Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Michael Bott
- From the Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany
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74
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Streptomyces lutosisoli sp. nov., a novel actinomycete isolated from muddy soil. Antonie van Leeuwenhoek 2018; 111:2403-2412. [PMID: 29995193 DOI: 10.1007/s10482-018-1129-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Accepted: 07/09/2018] [Indexed: 10/28/2022]
Abstract
A novel Gram-stain positive, spore-forming, aerobic actinomycete, designated strain NEAU-QTH3-11T, was isolated from muddy soil collected from a stream in Qitaihe, Heilongjiang Province, northeast China and characterised using a polyphasic approach. The 16S rRNA gene sequence analysis showed that strain NEAU-QTH3-11T belongs to the genus Streptomyces and is closely related to Streptomyces rhizosphaerihabitans NBRC 109807T (99.38%) and Streptomyces mirabilis JCM 4791T (99.03%). Phylogenetic analysis based on the 16S rRNA gene sequences indicated that the strain formed a cluster with S. rhizosphaerihabitans NBRC 109807T and Streptomyces siamensis NBRC 108799T (98.62%). The menaquinones were identified as MK-9(H8), MK-9(H6) and MK-9(H4). The phospholipid profile was found to consist of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, an unidentified phospholipid and an unidentified lipid. The major fatty acids were identified as anteiso-C15:0, iso-C16:0, C16:0 and C15:0. However, multilocus sequence analysis based on five house-keeping genes (atpD, gyrB, rpoB, recA and trpB), low DNA-DNA hybridization results and some phenotypic, physiological and biochemical properties could differentiate the strain from its close relatives in the genus Streptomyces. Therefore, strain NEAU-QTH3-11T is considered to represent a novel species of the genus Streptomyces, for which the name Streptomyces lutosisoli sp. nov. is proposed, with NEAU-QTH3-11T (=DSM 42165T=CGMCC 4.7198T) as the type strain.
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75
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Hu D, Cha G, Gao B. A Phylogenomic and Molecular Markers Based Analysis of the Class Acidimicrobiia. Front Microbiol 2018; 9:987. [PMID: 29867887 PMCID: PMC5962788 DOI: 10.3389/fmicb.2018.00987] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 04/27/2018] [Indexed: 01/22/2023] Open
Abstract
Recent metagenomic surveys of microbial community suggested that species associated with the class Acidimicrobiia are abundant in diverse aquatic environments such as acidic mine water, waste water sludge, freshwater, or marine habitats, but very few species have been cultivated and characterized. The current taxonomic framework of Acidimicrobiia is solely based on 16S rRNA sequence analysis of few cultivable representatives, and no molecular, biochemical, or physiological characteristics are known that can distinguish species of this class from the other bacteria. This study reports the phylogenomic analysis for 20 sequenced members of this class and reveals another three major lineages in addition to the two recognized families. Comparative analysis of the sequenced Acidimicrobiia species identified 15 conserved signature indels (CSIs) in widely distributed proteins and 26 conserved signature proteins (CSPs) that are either specific to this class as a whole or to its major lineages. This study represents the most comprehensive phylogenetic analysis of the class Acidimicrobiia and the identified CSIs and CSPs provide useful molecular markers for the identification and delineation of species belonging to this class or its subgroups.
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Affiliation(s)
- Danyu Hu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Guihong Cha
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Beile Gao
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
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76
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Streptomyces urticae sp. nov., isolated from rhizosphere soil of Urtica urens L. Antonie van Leeuwenhoek 2018; 111:1835-1843. [DOI: 10.1007/s10482-018-1072-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 03/20/2018] [Indexed: 10/17/2022]
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77
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Gupta RS, Sawnani S, Adeolu M, Alnajar S, Oren A. Phylogenetic framework for the phylum Tenericutes based on genome sequence data: proposal for the creation of a new order Mycoplasmoidales ord. nov., containing two new families Mycoplasmoidaceae fam. nov. and Metamycoplasmataceae fam. nov. harbouring Eperythrozoon, Ureaplasma and five novel genera. Antonie van Leeuwenhoek 2018; 111:1583-1630. [PMID: 29556819 DOI: 10.1007/s10482-018-1047-3] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 02/08/2018] [Indexed: 12/19/2022]
Abstract
The genus Mycoplasma, including species earlier classified in the genera Eperythrozoon and Haemobartonella, contains ~ 120 species and constitutes an extensively polyphyletic assemblage of bacteria within the phylum Tenericutes. Due to their small genome sizes and lack of unique characteristics, the relationships among the mycoplasmas/Tenericutes are not reliably discerned. Using genome sequences for 140 Tenericutes, their evolutionary relationships were examined using multiple independent approaches. Phylogenomic trees were constructed for 63 conserved proteins, 45 ribosomal proteins, three main subunits of RNA polymerase and 16S rRNA gene sequences. In all of these trees, Tenericutes species reliably grouped into four main clades designated as the "Acholeplasma", "Spiroplasma", "Pneumoniae" and "Hominis" clusters. These clades are also distinguished based on a similarity matrix constructed based on 16S rRNA gene sequences. Mycoplasma species were dispersed across 3 of these 4 clades highlighting their extensive polyphyly. In parallel, our comparative genomic analyses have identified > 100 conserved signature indels (CSIs) and 14 conserved signature proteins (CSPs), which are uniquely shared by the members of four identified clades, strongly supporting their monophyly and identifying them in molecular terms. Mycoplasma mycoides, the type species of the genus Mycoplasma, and a small number of other Mycoplasma species, formed a strongly supported clade within the "Spiroplasma" cluster. Nine CSIs and 14 CSPs reliably distinguish this clade from all other Mycoplasmatales species. The remainder of the Mycoplasmatales species are part of the "Pneumoniae" and "Hominis" clusters, which group together in phylogenetic trees. Here we are proposing that the order Mycoplasmatales should be emended to encompass only the Mycoplasma species within the "Spiroplasma" cluster and that a new order, Mycoplasmoidales ord. nov., should be created to encompass the other Mycoplasma species. The "Pneumoniae" and the "Hominis" clusters are proposed as two new families, Mycoplasmoidaceae fam. nov., which includes the genera Eperythrozoon, Ureaplasma, and the newly proposed genera Malacoplasma and Mycoplasmoides, and Metamycoplasmataceae fam. nov. to contain the newly proposed genera Metamycoplasma, Mycoplasmopsis, and Mesomycoplasma. The results presented here allow reliable discernment, both in phylogenetic and molecular terms, of the members of the two proposed families as well as different described genera within these families including members of the genus Eperythrozoon, which is comprised of uncultivable organisms. The taxonomic reclassifications proposed here, which more accurately portray the genetic diversity among the Tenericutes/Mycoplasma species, provide a new framework for understanding the biological and clinical aspects of these important microbes.
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Affiliation(s)
- Radhey S Gupta
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8N 3Z5, Canada.
| | - Sahil Sawnani
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8N 3Z5, Canada
| | - Mobolaji Adeolu
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8N 3Z5, Canada
| | - Seema Alnajar
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8N 3Z5, Canada
| | - Aharon Oren
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401, Jerusalem, Israel
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78
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Nezametdinova VZ, Mavletova DA, Alekseeva MG, Chekalina MS, Zakharevich NV, Danilenko VN. Species-specific serine-threonine protein kinase Pkb2 of Bifidobacterium longum subsp. longum: Genetic environment and substrate specificity. Anaerobe 2018. [PMID: 29534913 DOI: 10.1016/j.anaerobe.2018.03.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The objective of this study was to determine for phosphorylated substrates of the species-specific serine-threonine protein kinase (STPK) Pkb2 from Bifidobacterium longum subsp. longum GT15. Two approaches were employed: analyses of phosphorylated membrane vesicles protein spectra following kinase reactions and analyses of the genes surrounding pkb2. A bioinformatics analysis of the genes surrounding pkb2 found a species-specific gene cluster PFNA in the genomes of 34 different bifidobacterial species. The identified cluster consisted of 5-8 genes depending on the species. The first five genes are characteristic for all considered species. These are the following genes encoding serine-threonine protein kinase (pkb2), fibronectin type III domain-containing protein (fn3), AAA-ATPase (aaa-atp), hypothetical protein with DUF58 domain (duf58) and transglutaminase (tgm). The sixth (protein phosphatase, prpC), seventh (hypothetical protein, BLGT_RS02790), and eighth (FHA domain-containing protein, fha) genes are included in this cluster, but they are not found in all species. The operon organization of the PFNA gene cluster was confirmed with transcriptional analysis. AAA-ATPase, which is encoded by a gene of the PFNA gene cluster, was found to be a substrate of the STPK Pkb2. Fourteen AAA-ATPase sites (seven serine, six threonine, and one tyrosine) phosphorylated by STPK Pkb2 were revealed. Analysis of the spectra of phosphorylated membrane vesicles proteins allowed us to identify eleven proteins that were considered as possible Pkb2 substrates. They belong to several functional classes: proteins involved in transcription and translation; proteins of the F1-domain of the FoF1-ATPase; ABC-transporters; molecular chaperone GroEL; and glutamine synthase, GlnA1. All identified proteins were considered moonlighting proteins. Three out of 11 proteins (glutamine synthetase GlnA1 and FoF1-ATPase alpha and beta subunits) were selected for further in vitro phosphorylation assays and were shown to be phosphorylated by Pkb2. Four phosphorylated substrates of the species-specific STPK Pkb2 from B. longum subsp. longum GT15 were identified for the first time. They included the moonlighting protein glutamine synthase GlnA, FoF1-ATPase alpha and beta subunits, and the chaperone MoxR family of AAA-ATPase. The ability of bifidobacterial STPK to phosphorylate the substrate on serine, threonine, and tyrosine residues was shown for the first time.
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Affiliation(s)
- V Z Nezametdinova
- Laboratory of Genetics of Microorganisms, Vavilov Institute of General Genetics Russian Academy of Sciences, 3 Gubkin Street, 119991, GSP-1, Moscow, Russian Federation.
| | - D A Mavletova
- Laboratory of Genetics of Microorganisms, Vavilov Institute of General Genetics Russian Academy of Sciences, 3 Gubkin Street, 119991, GSP-1, Moscow, Russian Federation
| | - M G Alekseeva
- Laboratory of Genetics of Microorganisms, Vavilov Institute of General Genetics Russian Academy of Sciences, 3 Gubkin Street, 119991, GSP-1, Moscow, Russian Federation
| | - M S Chekalina
- Laboratory of Genetics of Microorganisms, Vavilov Institute of General Genetics Russian Academy of Sciences, 3 Gubkin Street, 119991, GSP-1, Moscow, Russian Federation
| | - N V Zakharevich
- Laboratory of Genetics of Microorganisms, Vavilov Institute of General Genetics Russian Academy of Sciences, 3 Gubkin Street, 119991, GSP-1, Moscow, Russian Federation
| | - V N Danilenko
- Laboratory of Genetics of Microorganisms, Vavilov Institute of General Genetics Russian Academy of Sciences, 3 Gubkin Street, 119991, GSP-1, Moscow, Russian Federation
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Gupta RS, Lo B, Son J. Phylogenomics and Comparative Genomic Studies Robustly Support Division of the Genus Mycobacterium into an Emended Genus Mycobacterium and Four Novel Genera. Front Microbiol 2018; 9:67. [PMID: 29497402 PMCID: PMC5819568 DOI: 10.3389/fmicb.2018.00067] [Citation(s) in RCA: 296] [Impact Index Per Article: 49.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Accepted: 01/11/2018] [Indexed: 01/08/2023] Open
Abstract
The genus Mycobacterium contains 188 species including several major human pathogens as well as numerous other environmental species. We report here comprehensive phylogenomics and comparative genomic analyses on 150 genomes of Mycobacterium species to understand their interrelationships. Phylogenetic trees were constructed for the 150 species based on 1941 core proteins for the genus Mycobacterium, 136 core proteins for the phylum Actinobacteria and 8 other conserved proteins. Additionally, the overall genome similarity amongst the Mycobacterium species was determined based on average amino acid identity of the conserved protein families. The results from these analyses consistently support the existence of five distinct monophyletic groups within the genus Mycobacterium at the highest level, which are designated as the "Tuberculosis-Simiae," "Terrae," "Triviale," "Fortuitum-Vaccae," and "Abscessus-Chelonae" clades. Some of these clades have also been observed in earlier phylogenetic studies. Of these clades, the "Abscessus-Chelonae" clade forms the deepest branching lineage and does not form a monophyletic grouping with the "Fortuitum-Vaccae" clade of fast-growing species. In parallel, our comparative analyses of proteins from mycobacterial genomes have identified 172 molecular signatures in the form of conserved signature indels and conserved signature proteins, which are uniquely shared by either all Mycobacterium species or by members of the five identified clades. The identified molecular signatures (or synapomorphies) provide strong independent evidence for the monophyly of the genus Mycobacterium and the five described clades and they provide reliable means for the demarcation of these clades and for their diagnostics. Based on the results of our comprehensive phylogenomic analyses and numerous identified molecular signatures, which consistently and strongly support the division of known mycobacterial species into the five described clades, we propose here division of the genus Mycobacterium into an emended genus Mycobacterium encompassing the "Tuberculosis-Simiae" clade, which includes all of the major human pathogens, and four novel genera viz. Mycolicibacterium gen. nov., Mycolicibacter gen. nov., Mycolicibacillus gen. nov. and Mycobacteroides gen. nov. corresponding to the "Fortuitum-Vaccae," "Terrae," "Triviale," and "Abscessus-Chelonae" clades, respectively. With the division of mycobacterial species into these five distinct groups, attention can now be focused on unique genetic and molecular characteristics that differentiate members of these groups.
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Affiliation(s)
- Radhey S. Gupta
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, CA, Canada
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Kleine B, Chattopadhyay A, Polen T, Pinto D, Mascher T, Bott M, Brocker M, Freudl R. The three-component system EsrISR regulates a cell envelope stress response in Corynebacterium glutamicum. Mol Microbiol 2017; 106:719-741. [PMID: 28922502 DOI: 10.1111/mmi.13839] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/13/2017] [Indexed: 02/03/2023]
Abstract
When the cell envelope integrity is compromised, bacteria trigger signaling cascades resulting in the production of proteins that counteract these extracytoplasmic stresses. Here, we show that the two-component system EsrSR regulates a cell envelope stress response in the Actinobacterium Corynebacterium glutamicum. The sensor kinase EsrS possesses an amino-terminal phage shock protein C (PspC) domain, a property that sets EsrSR apart from all other two-component systems characterized so far. An integral membrane protein, EsrI, whose gene is divergently transcribed to the esrSR gene locus and which interestingly also possesses a PspC domain, acts as an inhibitor of EsrSR under non-stress conditions. The resulting EsrISR three-component system is activated among others by antibiotics inhibiting the lipid II cycle, such as bacitracin and vancomycin, and it orchestrates a broad regulon including the esrI-esrSR gene locus itself, genes encoding heat shock proteins, ABC transporters, and several putative membrane-associated or secreted proteins of unknown function. Among those, the ABC transporter encoded by cg3322-3320 was shown to be directly involved in bacitracin resistance of C. glutamicum. Since similar esrI-esrSR loci are present in a large number of actinobacterial genomes, EsrISR represents a novel type of stress-responsive system whose components are highly conserved in the phylum Actinobacteria.
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Affiliation(s)
- Britta Kleine
- Institut für Bio- und Geowissenschaften 1, Biotechnologie, Forschungszentrum Jülich GmbH, Jülich D-52425, Germany
| | - Ava Chattopadhyay
- Institut für Bio- und Geowissenschaften 1, Biotechnologie, Forschungszentrum Jülich GmbH, Jülich D-52425, Germany
| | - Tino Polen
- Institut für Bio- und Geowissenschaften 1, Biotechnologie, Forschungszentrum Jülich GmbH, Jülich D-52425, Germany
| | - Daniela Pinto
- Institut für Mikrobiologie, Technische Universität Dresden, Zellescher Weg 20b, Dresden D-01217, Germany
| | - Thorsten Mascher
- Institut für Mikrobiologie, Technische Universität Dresden, Zellescher Weg 20b, Dresden D-01217, Germany
| | - Michael Bott
- Institut für Bio- und Geowissenschaften 1, Biotechnologie, Forschungszentrum Jülich GmbH, Jülich D-52425, Germany
| | - Melanie Brocker
- Institut für Bio- und Geowissenschaften 1, Biotechnologie, Forschungszentrum Jülich GmbH, Jülich D-52425, Germany
| | - Roland Freudl
- Institut für Bio- und Geowissenschaften 1, Biotechnologie, Forschungszentrum Jülich GmbH, Jülich D-52425, Germany
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81
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Oliveira A, Oliveira LC, Aburjaile F, Benevides L, Tiwari S, Jamal SB, Silva A, Figueiredo HCP, Ghosh P, Portela RW, De Carvalho Azevedo VA, Wattam AR. Insight of Genus Corynebacterium: Ascertaining the Role of Pathogenic and Non-pathogenic Species. Front Microbiol 2017; 8:1937. [PMID: 29075239 PMCID: PMC5643470 DOI: 10.3389/fmicb.2017.01937] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 09/21/2017] [Indexed: 11/22/2022] Open
Abstract
This review gathers recent information about genomic and transcriptomic studies in the Corynebacterium genus, exploring, for example, prediction of pathogenicity islands and stress response in different pathogenic and non-pathogenic species. In addition, is described several phylogeny studies to Corynebacterium, exploring since the identification of species until biological speciation in one species belonging to the genus Corynebacterium. Important concepts associated with virulence highlighting the role of Pld protein and Tox gene. The adhesion, characteristic of virulence factor, was described using the sortase mechanism that is associated to anchorage to the cell wall. In addition, survival inside the host cell and some diseases, were too addressed for pathogenic corynebacteria, while important biochemical pathways and biotechnological applications retain the focus of this review for non-pathogenic corynebacteria. Concluding, this review broadly explores characteristics in genus Corynebacterium showing to have strong relevance inside the medical, veterinary, and biotechnology field.
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Affiliation(s)
- Alberto Oliveira
- Molecular and Cellular Laboratory, General Biology Department, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Leticia C Oliveira
- Molecular and Cellular Laboratory, General Biology Department, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Flavia Aburjaile
- Center of Genomics and System Biology, Federal University of Pará, Belém, Brazil
| | - Leandro Benevides
- Molecular and Cellular Laboratory, General Biology Department, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Sandeep Tiwari
- Molecular and Cellular Laboratory, General Biology Department, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Syed B Jamal
- Molecular and Cellular Laboratory, General Biology Department, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Arthur Silva
- Center of Genomics and System Biology, Federal University of Pará, Belém, Brazil
| | - Henrique C P Figueiredo
- Aquacen, National Reference Laboratory for Aquatic Animal Diseases, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Preetam Ghosh
- Department of Computational Science, Virginia Commonwealth University, Richmond, VA, United States
| | - Ricardo W Portela
- Laboratory of Immunology and Molecular Bióloga, Health Sciences Institute, Federal University of Bahiaa, Salvador, Brazil
| | - Vasco A De Carvalho Azevedo
- Molecular and Cellular Laboratory, General Biology Department, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Alice R Wattam
- Biocomplexity Institute of Virginia Tech, Virginia Tech, Blacksburg, VA, United States
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82
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Gomes KM, Duarte RS, de Freire Bastos MDC. Lantibiotics produced by Actinobacteria and their potential applications (a review). MICROBIOLOGY-SGM 2017; 163:109-121. [PMID: 28270262 DOI: 10.1099/mic.0.000397] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The phylum Actinobacteria, which comprises a great variety of Gram-positive bacteria with a high G+C content in their genomes, is known for its large production of bioactive compounds, including those with antimicrobial activity. Among the antimicrobials, bacteriocins, ribosomally synthesized peptides, represent an important arsenal of potential new drugs to face the increasing prevalence of resistance to antibiotics among microbial pathogens. The actinobacterial bacteriocins form a heterogeneous group of substances that is difficult to adapt to most proposed classification schemes. However, recent updates have accommodated efficiently the diversity of bacteriocins produced by this phylum. Among the bacteriocins, the lantibiotics represent a source of new antimicrobials to control infections caused mainly by Gram-positive bacteria and with a low propensity for resistance development. Moreover, some of these compounds have additional biological properties, exhibiting activity against viruses and tumour cells and having also potential to be used in blood pressure or inflammation control and in pain relief. Thus, lantibiotics already described in Actinobacteria exhibit potential practical applications in medical settings, food industry and agriculture, with examples at different stages of pre-clinical and clinical trials.
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Affiliation(s)
- Karen Machado Gomes
- Departamento de Microbiologia Médica, Instituto de Microbiologia Paulo de Góes, UFRJ, Rio de Janeiro, Brazil
| | - Rafael Silva Duarte
- Departamento de Microbiologia Médica, Instituto de Microbiologia Paulo de Góes, UFRJ, Rio de Janeiro, Brazil
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83
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Human ZR, Crous CJ, Roets F, Venter SN, Wingfield MJ, de Beer ZW. Biodiversity and ecology of flower-associated actinomycetes in different flowering stages of Protea repens. Antonie van Leeuwenhoek 2017; 111:209-226. [PMID: 28936706 DOI: 10.1007/s10482-017-0942-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 09/06/2017] [Indexed: 02/07/2023]
Abstract
Actinomycete bacteria have previously been reported from reproductive structures (infructescences) of Protea (sugarbush/suikerbos) species, a niche dominated by fungi in the genera Knoxdaviesia and Sporothrix. It is probable that these taxa have symbiotic interactions, but a lack of knowledge regarding their diversity and general ecology precludes their study. We determined the diversity of actinomycetes within Protea repens inflorescence buds, open inflorescences, young and mature infructescences, and leaf litter surrounding these trees. Since the P. repens habitat is fire-prone, we also considered the potential of these bacteria to recolonise infructescences after fire. Actinomycetes were largely absent from flower buds and inflorescences but were consistently present in young and mature infructescences. Two Streptomyces spp. were the most consistent taxa recovered, one of which was also routinely isolated from leaf litter. Lower colonisation rates were evident in samples from a recently burnt site. One of the most consistent taxa isolated from older trees in the unburnt site was absent from this site. Our findings show that P. repens has a distinct community of actinomycetes dominated by a few species. These communities change over time and infructescence developmental stage, season and the age of the host population. Mature infructescences appear to be important sources of inoculum for some of the actinomycetes, seemingly disrupted by fire. Increased fire frequency limiting maturation of P. repens infructescences could thus impact future actinomycete colonisation in the landscape. Streptomyces spp. are likely to share this niche with the ophiostomatoid fungi, which merits further study regarding their interactions and mode of transfer.
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Affiliation(s)
- Zander R Human
- Department of Microbiology and Plant Pathology, Forestry and Agriculture Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Casparus J Crous
- Department of Plant and Soil Sciences, Forestry and Agriculture Biotechnology Institute, University of Pretoria, Pretoria, South Africa.,Faculdade de Ciências, Centre for Ecology, Evolution and Environmental Changes (cE3c), Universidade de Lisboa, Campo Grande, 1749-016, Lisbon, Portugal
| | - Francois Roets
- Department of Conservation Ecology and Entomology, Stellenbosch University, Private Bag X1, Stellenbosch, 7600, South Africa
| | - Stephanus N Venter
- Department of Microbiology and Plant Pathology, Forestry and Agriculture Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Michael J Wingfield
- Department of Microbiology and Plant Pathology, Forestry and Agriculture Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Z Wilhelm de Beer
- Department of Microbiology and Plant Pathology, Forestry and Agriculture Biotechnology Institute, University of Pretoria, Pretoria, South Africa.
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84
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Metabolic Network Analysis and Metatranscriptomics Reveal Auxotrophies and Nutrient Sources of the Cosmopolitan Freshwater Microbial Lineage acI. mSystems 2017; 2:mSystems00091-17. [PMID: 28861526 PMCID: PMC5574706 DOI: 10.1128/msystems.00091-17] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 08/08/2017] [Indexed: 11/20/2022] Open
Abstract
The metabolic activity of uncultivated microorganisms contributes to numerous ecosystem processes, ranging from nutrient cycling in the environment to influencing human health and disease. Advances in sequencing technology have enabled the assembly of genomes for these microorganisms, but our ability to generate reference genomes far outstrips our ability to analyze them. Common approaches to analyzing microbial metabolism require reconstructing the entirety of an organism’s metabolic pathways or performing targeted searches for genes involved in a specific process. This paper presents a third approach, in which draft metabolic reconstructions are used to identify compounds through which an organism may interact with its environment. These compounds can then guide more-intensive metabolic reconstruction efforts and can also provide new hypotheses about the specific contributions that microbes make to ecosystem-scale metabolic processes. An explosion in the number of available genome sequences obtained through metagenomics and single-cell genomics has enabled a new view of the diversity of microbial life, yet we know surprisingly little about how microbes interact with each other or their environment. In fact, the majority of microbial species remain uncultivated, while our perception of their ecological niches is based on reconstruction of their metabolic potential. In this work, we demonstrate how the “seed set framework,” which computes the set of compounds that an organism must acquire from its environment (E. Borenstein, M. Kupiec, M. W. Feldman, and E. Ruppin, Proc Natl Acad Sci U S A 105:14482–14487, 2008, https://doi.org/10.1073/pnas.0806162105), enables computational analysis of metabolic reconstructions while providing new insights into a microbe’s metabolic capabilities, such as nutrient use and auxotrophies. We apply this framework to members of the ubiquitous freshwater actinobacterial lineage acI, confirming and extending previous experimental and genomic observations implying that acI bacteria are heterotrophs reliant on peptides and saccharides. We also present the first metatranscriptomic study of the acI lineage, revealing high expression of transport proteins and the light-harvesting protein actinorhodopsin. Putative transport proteins complement predictions of nutrients and essential metabolites while providing additional support of the hypothesis that members of the acI are photoheterotrophs. IMPORTANCE The metabolic activity of uncultivated microorganisms contributes to numerous ecosystem processes, ranging from nutrient cycling in the environment to influencing human health and disease. Advances in sequencing technology have enabled the assembly of genomes for these microorganisms, but our ability to generate reference genomes far outstrips our ability to analyze them. Common approaches to analyzing microbial metabolism require reconstructing the entirety of an organism’s metabolic pathways or performing targeted searches for genes involved in a specific process. This paper presents a third approach, in which draft metabolic reconstructions are used to identify compounds through which an organism may interact with its environment. These compounds can then guide more-intensive metabolic reconstruction efforts and can also provide new hypotheses about the specific contributions that microbes make to ecosystem-scale metabolic processes.
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85
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Stefanaki C, Peppa M, Mastorakos G, Chrousos GP. Examining the gut bacteriome, virome, and mycobiome in glucose metabolism disorders: Are we on the right track? Metabolism 2017; 73:52-66. [PMID: 28732571 DOI: 10.1016/j.metabol.2017.04.014] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Revised: 04/21/2017] [Accepted: 04/28/2017] [Indexed: 12/19/2022]
Abstract
Human gut microbiome is defined as the gene complement of the gut microbial community, measured via laboratory metagenomic techniques. It includes bacteriome, virome and mycobiome, which represent, respectively, the assemblages of bacteria, viruses and fungi, living in the human gut. Gut microbiota function as a living "organ" that interacts with the gastro-intestinal environment, provides nutrients and vitamins to the organism and transduces hormonal messages, essentially influencing the main metabolic pathways, including drug metabolism. A clear association between gut, and glucose metabolism disorders has recently emerged. Medications acting on glucose absorption in the gut, or enhancing gut hormone activity are already extensively employed in the therapy of diabetes. Moreover, the gut is characterized by immune, and autonomous neuronal features, which play a critical role in maintaining glucose metabolism homeostasis. Gut microbes respond to neuroendocrine, and immune biochemical messages, affecting the health, and behavior of the host. There is vast heterogeneity in the studies included in this review, hence a meta-analysis, or a systematic review were not applicable. In this article, we attempt to reveal the interplay between human gut microbiota physiology, and hyperglycemic states, synthesizing, and interpreting findings from human studies.
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Affiliation(s)
- Charikleia Stefanaki
- 1st Department of Pediatrics, Choremeio Research Laboratory, Athens University Medical School, National and Kapodistrian University of Athens, Medical School, Athens, Greece.
| | - Melpomeni Peppa
- Endocrine Unit, 2nd Department of Internal Medicine Propaedeutic, Research Institute and Diabetes Center, National and Kapodistrian University of Athens, Attikon University Hospital, Athens, Greece
| | - George Mastorakos
- Department of Endocrinology, Metabolism and Diabetes, Aretaieion University Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - George P Chrousos
- 1st Department of Pediatrics, Choremeio Research Laboratory, Athens University Medical School, National and Kapodistrian University of Athens, Medical School, Athens, Greece
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86
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Alnajar S, Khadka B, Gupta RS. Ribonucleotide Reductases from Bifidobacteria Contain Multiple Conserved Indels Distinguishing Them from All Other Organisms: In Silico Analysis of the Possible Role of a 43 aa Bifidobacteria-Specific Insert in the Class III RNR Homolog. Front Microbiol 2017; 8:1409. [PMID: 28824557 PMCID: PMC5535262 DOI: 10.3389/fmicb.2017.01409] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Accepted: 07/11/2017] [Indexed: 01/05/2023] Open
Abstract
Bifidobacteria comprises an important group/order of bacteria whose members have widespread usage in the food and health industry due to their health-promoting activity in the human gastrointestinal tract. However, little is known about the underlying molecular properties that are responsible for the probiotic effects of these bacteria. The enzyme ribonucleotide reductase (RNR) plays a key role in all organisms by reducing nucleoside di- or tri- phosphates into corresponding deoxyribose derivatives required for DNA synthesis, and RNR homologs belonging to classes I and III are present in either most or all Bifidobacteriales. Comparative analyses of these RNR homologs have identified several novel sequence features in the forms of conserved signature indels (CSIs) that are exclusively found in bifidobacterial RNRs. Specifically, in the large subunit of the aerobic class Ib RNR, three CSIs have been identified that are uniquely found in the Bifidobacteriales homologs. Similarly, the large subunit of the anaerobic class III RNR contains five CSIs that are also distinctive characteristics of bifidobacteria. Phylogenetic analyses indicate that these CSIs were introduced in a common ancestor of the Bifidobacteriales and retained by all descendants, likely due to their conferring advantageous functional roles. The identified CSIs in the bifidobacterial RNR homologs provide useful tools for further exploration of the novel functional aspects of these important enzymes that are exclusive to these bacteria. We also report here the results of homology modeling studies, which indicate that most of the bifidobacteria-specific CSIs are located within the surface loops of the RNRs, and of these, a large 43 amino acid insert in the class III RNR homolog forms an extension of the allosteric regulatory site known to be essential for protein function. Preliminary docking studies suggest that this large CSI may be playing a role in enhancing the stability of the RNR dimer complex. The possible significances of the identified CSIs, as well as the distribution of RNR homologs in the Bifidobacteriales, are discussed.
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Affiliation(s)
- Seema Alnajar
- Department of Biochemistry and Biomedical Sciences, McMaster University, HamiltonON, Canada
| | - Bijendra Khadka
- Department of Biochemistry and Biomedical Sciences, McMaster University, HamiltonON, Canada
| | - Radhey S Gupta
- Department of Biochemistry and Biomedical Sciences, McMaster University, HamiltonON, Canada
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87
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Lewin GR, Carlos C, Chevrette MG, Horn HA, McDonald BR, Stankey RJ, Fox BG, Currie CR. Evolution and Ecology of Actinobacteria and Their Bioenergy Applications. Annu Rev Microbiol 2017; 70:235-54. [PMID: 27607553 DOI: 10.1146/annurev-micro-102215-095748] [Citation(s) in RCA: 163] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The ancient phylum Actinobacteria is composed of phylogenetically and physiologically diverse bacteria that help Earth's ecosystems function. As free-living organisms and symbionts of herbivorous animals, Actinobacteria contribute to the global carbon cycle through the breakdown of plant biomass. In addition, they mediate community dynamics as producers of small molecules with diverse biological activities. Together, the evolution of high cellulolytic ability and diverse chemistry, shaped by their ecological roles in nature, make Actinobacteria a promising group for the bioenergy industry. Specifically, their enzymes can contribute to industrial-scale breakdown of cellulosic plant biomass into simple sugars that can then be converted into biofuels. Furthermore, harnessing their ability to biosynthesize a range of small molecules has potential for the production of specialty biofuels.
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Affiliation(s)
- Gina R Lewin
- Department of Bacteriology, University of Wisconsin-Madison, Wisconsin 53706; .,Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
| | - Camila Carlos
- Department of Bacteriology, University of Wisconsin-Madison, Wisconsin 53706; .,Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
| | - Marc G Chevrette
- Department of Bacteriology, University of Wisconsin-Madison, Wisconsin 53706; .,Department of Genetics, University of Wisconsin-Madison, Wisconsin 53706
| | - Heidi A Horn
- Department of Bacteriology, University of Wisconsin-Madison, Wisconsin 53706;
| | - Bradon R McDonald
- Department of Bacteriology, University of Wisconsin-Madison, Wisconsin 53706; .,Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
| | - Robert J Stankey
- Department of Bacteriology, University of Wisconsin-Madison, Wisconsin 53706; .,Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
| | - Brian G Fox
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726.,Department of Biochemistry, University of Wisconsin-Madison, Wisconsin 53706
| | - Cameron R Currie
- Department of Bacteriology, University of Wisconsin-Madison, Wisconsin 53706; .,Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
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Kulis-Horn RK, Rückert C, Kalinowski J, Persicke M. Sequence-based identification of inositol monophosphatase-like histidinol-phosphate phosphatases (HisN) in Corynebacterium glutamicum, Actinobacteria, and beyond. BMC Microbiol 2017; 17:161. [PMID: 28720084 PMCID: PMC5516325 DOI: 10.1186/s12866-017-1069-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 07/10/2017] [Indexed: 12/30/2022] Open
Abstract
Background The eighth step of l-histidine biosynthesis is carried out by an enzyme called histidinol-phosphate phosphatase (HolPase). Three unrelated HolPase families are known so far. Two of them are well studied: HAD-type HolPases known from Gammaproteobacteria like Escherichia coli or Salmonella enterica and PHP-type HolPases known from yeast and Firmicutes like Bacillus subtilis. However, the third family of HolPases, the inositol monophosphatase (IMPase)-like HolPases, present in Actinobacteria like Corynebacterium glutamicum (HisN) and plants, are poorly characterized. Moreover, there exist several IMPase-like proteins in bacteria (e.g. CysQ, ImpA, and SuhB) which are very similar to HisN but most likely do not participate in l-histidine biosynthesis. Results Deletion of hisN, the gene encoding the IMPase-like HolPase in C. glutamicum, does not result in complete l-histidine auxotrophy. Out of four hisN homologs present in the genome of C. glutamicum (impA, suhB, cysQ, and cg0911), only cg0911 encodes an enzyme with HolPase activity. The enzymatic properties of HisN and Cg0911 were determined, delivering the first available kinetic data for IMPase-like HolPases. Additionally, we analyzed the amino acid sequences of potential HisN, ImpA, SuhB, CysQ and Cg0911 orthologs from bacteria and identified six conserved sequence motifs for each group of orthologs. Mutational studies confirmed the importance of a highly conserved aspartate residue accompanied by several aromatic amino acid residues present in motif 5 for HolPase activity. Several bacterial proteins containing all identified HolPase motifs, but showing only moderate sequence similarity to HisN from C. glutamicum, were experimentally confirmed as IMPase-like HolPases, demonstrating the value of the identified motifs. Based on the confirmed IMPase-like HolPases two profile Hidden Markov Models (HMMs) were build using an iterative approach. These HMMs allow the fast, reliable detection and differentiation of the two paralog groups from each other and other IMPases. Conclusion The kinetic data obtained for HisN from C. glutamicum, as an example for an IMPase-like HolPases, shows remarkable differences in enzyme properties as compared to HAD- or PHP-type HolPases. The six sequence motifs and the HMMs presented in this study can be used to reliably differentiate between IMPase-like HolPases and IMPase-like proteins with no such activity, with the potential to enhance current and future genome annotations. A phylogenetic analysis reveals that IMPase-like HolPases are not only present in Actinobacteria and plant but can be found in further bacterial phyla, including, among others, Proteobacteria, Chlorobi and Planctomycetes. Electronic supplementary material The online version of this article (doi:10.1186/s12866-017-1069-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Robert Kasimir Kulis-Horn
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615, Bielefeld, Germany
| | - Christian Rückert
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615, Bielefeld, Germany
| | - Jörn Kalinowski
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615, Bielefeld, Germany
| | - Marcus Persicke
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615, Bielefeld, Germany.
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Klyczek KK, Bonilla JA, Jacobs-Sera D, Adair TL, Afram P, Allen KG, Archambault ML, Aziz RM, Bagnasco FG, Ball SL, Barrett NA, Benjamin RC, Blasi CJ, Borst K, Braun MA, Broomell H, Brown CB, Brynell ZS, Bue AB, Burke SO, Casazza W, Cautela JA, Chen K, Chimalakonda NS, Chudoff D, Connor JA, Cross TS, Curtis KN, Dahlke JA, Deaton BM, Degroote SJ, DeNigris DM, DeRuff KC, Dolan M, Dunbar D, Egan MS, Evans DR, Fahnestock AK, Farooq A, Finn G, Fratus CR, Gaffney BL, Garlena RA, Garrigan KE, Gibbon BC, Goedde MA, Guerrero Bustamante CA, Harrison M, Hartwell MC, Heckman EL, Huang J, Hughes LE, Hyduchak KM, Jacob AE, Kaku M, Karstens AW, Kenna MA, Khetarpal S, King RA, Kobokovich AL, Kolev H, Konde SA, Kriese E, Lamey ME, Lantz CN, Lapin JS, Lawson TO, Lee IY, Lee SM, Lee-Soety JY, Lehmann EM, London SC, Lopez AJ, Lynch KC, Mageeney CM, Martynyuk T, Mathew KJ, Mavrich TN, McDaniel CM, McDonald H, McManus CJ, Medrano JE, Mele FE, Menninger JE, Miller SN, Minick JE, Nabua CT, Napoli CK, Nkangabwa M, Oates EA, Ott CT, Pellerino SK, Pinamont WJ, Pirnie RT, Pizzorno MC, Plautz EJ, Pope WH, Pruett KM, Rickstrew G, Rimple PA, Rinehart CA, Robinson KM, Rose VA, Russell DA, Schick AM, Schlossman J, Schneider VM, Sells CA, Sieker JW, Silva MP, Silvi MM, Simon SE, Staples AK, Steed IL, Stowe EL, Stueven NA, Swartz PT, Sweet EA, Sweetman AT, Tender C, Terry K, Thomas C, Thomas DS, Thompson AR, Vanderveen L, Varma R, Vaught HL, Vo QD, Vonberg ZT, Ware VC, Warrad YM, Wathen KE, Weinstein JL, Wyper JF, Yankauskas JR, Zhang C, Hatfull GF. Tales of diversity: Genomic and morphological characteristics of forty-six Arthrobacter phages. PLoS One 2017; 12:e0180517. [PMID: 28715480 PMCID: PMC5513430 DOI: 10.1371/journal.pone.0180517] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 06/17/2017] [Indexed: 11/19/2022] Open
Abstract
The vast bacteriophage population harbors an immense reservoir of genetic information. Almost 2000 phage genomes have been sequenced from phages infecting hosts in the phylum Actinobacteria, and analysis of these genomes reveals substantial diversity, pervasive mosaicism, and novel mechanisms for phage replication and lysogeny. Here, we describe the isolation and genomic characterization of 46 phages from environmental samples at various geographic locations in the U.S. infecting a single Arthrobacter sp. strain. These phages include representatives of all three virion morphologies, and Jasmine is the first sequenced podovirus of an actinobacterial host. The phages also span considerable sequence diversity, and can be grouped into 10 clusters according to their nucleotide diversity, and two singletons each with no close relatives. However, the clusters/singletons appear to be genomically well separated from each other, and relatively few genes are shared between clusters. Genome size varies from among the smallest of siphoviral phages (15,319 bp) to over 70 kbp, and G+C contents range from 45-68%, compared to 63.4% for the host genome. Although temperate phages are common among other actinobacterial hosts, these Arthrobacter phages are primarily lytic, and only the singleton Galaxy is likely temperate.
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Affiliation(s)
- Karen K. Klyczek
- Biology Department, University of Wisconsin-River Falls, River Falls, Wisconsin, United States of America
| | - J. Alfred Bonilla
- Biology Department, University of Wisconsin-River Falls, River Falls, Wisconsin, United States of America
| | - Deborah Jacobs-Sera
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Tamarah L. Adair
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - Patricia Afram
- Department of Science, Cabrini University, Radnor, Pennsylvania, United States of America
| | - Katherine G. Allen
- Biology Department, Western Kentucky University, Bowling Green, Kentucky, United States of America
| | - Megan L. Archambault
- Biology Department, University of Wisconsin-River Falls, River Falls, Wisconsin, United States of America
| | - Rahat M. Aziz
- Department of Biological Sciences, University of North Texas, Denton, Texas, United States of America
| | - Filippa G. Bagnasco
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - Sarah L. Ball
- Center for Life Sciences Education, The Ohio State University, Columbus, Ohio, United States of America
| | - Natalie A. Barrett
- Biology Department, Saint Joseph’s University, Philadelphia, Pennsylvania, United States of America
| | - Robert C. Benjamin
- Department of Biological Sciences, University of North Texas, Denton, Texas, United States of America
| | - Christopher J. Blasi
- Biology Department, Bucknell University, Lewisburg, Pennsylvania, United States of America
| | - Katherine Borst
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Mary A. Braun
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Haley Broomell
- Department of Science, Cabrini University, Radnor, Pennsylvania, United States of America
| | - Conner B. Brown
- Biology Department, Western Kentucky University, Bowling Green, Kentucky, United States of America
| | - Zachary S. Brynell
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - Ashley B. Bue
- Biology Department, University of Wisconsin-River Falls, River Falls, Wisconsin, United States of America
| | - Sydney O. Burke
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - William Casazza
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Julia A. Cautela
- Biology Department, Saint Joseph’s University, Philadelphia, Pennsylvania, United States of America
| | - Kevin Chen
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | | | - Dylan Chudoff
- Department of Science, Cabrini University, Radnor, Pennsylvania, United States of America
| | - Jade A. Connor
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - Trevor S. Cross
- Department of Science, Cabrini University, Radnor, Pennsylvania, United States of America
| | - Kyra N. Curtis
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - Jessica A. Dahlke
- Biology Department, University of Wisconsin-River Falls, River Falls, Wisconsin, United States of America
| | - Bethany M. Deaton
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - Sarah J. Degroote
- Biology Department, University of Wisconsin-River Falls, River Falls, Wisconsin, United States of America
| | - Danielle M. DeNigris
- Biology Department, Saint Joseph’s University, Philadelphia, Pennsylvania, United States of America
| | - Katherine C. DeRuff
- Biology Department, Bucknell University, Lewisburg, Pennsylvania, United States of America
| | - Milan Dolan
- Biology Department, Western Kentucky University, Bowling Green, Kentucky, United States of America
| | - David Dunbar
- Department of Science, Cabrini University, Radnor, Pennsylvania, United States of America
| | - Marisa S. Egan
- Biology Department, Saint Joseph’s University, Philadelphia, Pennsylvania, United States of America
| | - Daniel R. Evans
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Abby K. Fahnestock
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - Amal Farooq
- Department of Biological Sciences, University of North Texas, Denton, Texas, United States of America
| | - Garrett Finn
- Biology Department, University of Wisconsin-River Falls, River Falls, Wisconsin, United States of America
| | | | - Bobby L. Gaffney
- Biology Department, Western Kentucky University, Bowling Green, Kentucky, United States of America
| | - Rebecca A. Garlena
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Kelly E. Garrigan
- Biology Department, Saint Joseph’s University, Philadelphia, Pennsylvania, United States of America
| | - Bryan C. Gibbon
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - Michael A. Goedde
- Biology Department, Western Kentucky University, Bowling Green, Kentucky, United States of America
| | | | - Melinda Harrison
- Department of Science, Cabrini University, Radnor, Pennsylvania, United States of America
| | - Megan C. Hartwell
- Biology Department, Saint Joseph’s University, Philadelphia, Pennsylvania, United States of America
| | - Emily L. Heckman
- Biological Sciences, Lehigh University, Bethlehem, Pennsylvania, United States of America
| | - Jennifer Huang
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Lee E. Hughes
- Department of Biological Sciences, University of North Texas, Denton, Texas, United States of America
| | - Kathryn M. Hyduchak
- Biology Department, Saint Joseph’s University, Philadelphia, Pennsylvania, United States of America
| | - Aswathi E. Jacob
- Biology Department, Saint Joseph’s University, Philadelphia, Pennsylvania, United States of America
| | - Machika Kaku
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Allen W. Karstens
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - Margaret A. Kenna
- Biological Sciences, Lehigh University, Bethlehem, Pennsylvania, United States of America
| | - Susheel Khetarpal
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Rodney A. King
- Biology Department, Western Kentucky University, Bowling Green, Kentucky, United States of America
| | - Amanda L. Kobokovich
- Biology Department, Bucknell University, Lewisburg, Pennsylvania, United States of America
| | - Hannah Kolev
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Sai A. Konde
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - Elizabeth Kriese
- Biology Department, University of Wisconsin-River Falls, River Falls, Wisconsin, United States of America
| | - Morgan E. Lamey
- Biology Department, Saint Joseph’s University, Philadelphia, Pennsylvania, United States of America
| | - Carter N. Lantz
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - Jonathan S. Lapin
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Temiloluwa O. Lawson
- Biology Department, University of Wisconsin-River Falls, River Falls, Wisconsin, United States of America
| | - In Young Lee
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Scott M. Lee
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - Julia Y. Lee-Soety
- Biology Department, Saint Joseph’s University, Philadelphia, Pennsylvania, United States of America
| | - Emily M. Lehmann
- Biology Department, University of Wisconsin-River Falls, River Falls, Wisconsin, United States of America
| | - Shawn C. London
- Biology Department, Saint Joseph’s University, Philadelphia, Pennsylvania, United States of America
| | - A. Javier Lopez
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Kelly C. Lynch
- Biology Department, Western Kentucky University, Bowling Green, Kentucky, United States of America
| | - Catherine M. Mageeney
- Biological Sciences, Lehigh University, Bethlehem, Pennsylvania, United States of America
| | - Tetyana Martynyuk
- Biology Department, Saint Joseph’s University, Philadelphia, Pennsylvania, United States of America
| | - Kevin J. Mathew
- Department of Biological Sciences, University of North Texas, Denton, Texas, United States of America
| | - Travis N. Mavrich
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Christopher M. McDaniel
- Biology Department, Western Kentucky University, Bowling Green, Kentucky, United States of America
| | - Hannah McDonald
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - C. Joel McManus
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Jessica E. Medrano
- Biology Department, Bucknell University, Lewisburg, Pennsylvania, United States of America
| | - Francis E. Mele
- Biology Department, Saint Joseph’s University, Philadelphia, Pennsylvania, United States of America
| | - Jennifer E. Menninger
- Biology Department, Saint Joseph’s University, Philadelphia, Pennsylvania, United States of America
| | - Sierra N. Miller
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - Josephine E. Minick
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - Courtney T. Nabua
- Biology Department, Saint Joseph’s University, Philadelphia, Pennsylvania, United States of America
| | - Caroline K. Napoli
- Biology Department, Saint Joseph’s University, Philadelphia, Pennsylvania, United States of America
| | - Martha Nkangabwa
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Elizabeth A. Oates
- Biology Department, Western Kentucky University, Bowling Green, Kentucky, United States of America
| | - Cassandra T. Ott
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Sarah K. Pellerino
- Biology Department, University of Wisconsin-River Falls, River Falls, Wisconsin, United States of America
| | - William J. Pinamont
- Biology Department, Bucknell University, Lewisburg, Pennsylvania, United States of America
| | - Ross T. Pirnie
- Biology Department, Bucknell University, Lewisburg, Pennsylvania, United States of America
| | - Marie C. Pizzorno
- Biology Department, Bucknell University, Lewisburg, Pennsylvania, United States of America
| | - Emilee J. Plautz
- Biology Department, University of Wisconsin-River Falls, River Falls, Wisconsin, United States of America
| | - Welkin H. Pope
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Katelyn M. Pruett
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - Gabbi Rickstrew
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Patrick A. Rimple
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Claire A. Rinehart
- Biology Department, Western Kentucky University, Bowling Green, Kentucky, United States of America
| | - Kayla M. Robinson
- Department of Biological Sciences, University of North Texas, Denton, Texas, United States of America
| | - Victoria A. Rose
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - Daniel A. Russell
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Amelia M. Schick
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - Julia Schlossman
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Victoria M. Schneider
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Chloe A. Sells
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - Jeremy W. Sieker
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - Morgan P. Silva
- Department of Biological Sciences, University of North Texas, Denton, Texas, United States of America
| | - Marissa M. Silvi
- Biology Department, Bucknell University, Lewisburg, Pennsylvania, United States of America
| | - Stephanie E. Simon
- Department of Biological Sciences, University of North Texas, Denton, Texas, United States of America
| | - Amanda K. Staples
- Biology Department, Western Kentucky University, Bowling Green, Kentucky, United States of America
| | - Isabelle L. Steed
- Biology Department, University of Wisconsin-River Falls, River Falls, Wisconsin, United States of America
| | - Emily L. Stowe
- Biology Department, Bucknell University, Lewisburg, Pennsylvania, United States of America
| | - Noah A. Stueven
- Biology Department, University of Wisconsin-River Falls, River Falls, Wisconsin, United States of America
| | - Porter T. Swartz
- Biology Department, University of Wisconsin-River Falls, River Falls, Wisconsin, United States of America
| | - Emma A. Sweet
- Biology Department, University of Wisconsin-River Falls, River Falls, Wisconsin, United States of America
| | - Abigail T. Sweetman
- Biology Department, Saint Joseph’s University, Philadelphia, Pennsylvania, United States of America
| | - Corrina Tender
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Katrina Terry
- Department of Science, Cabrini University, Radnor, Pennsylvania, United States of America
| | - Chrystal Thomas
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Daniel S. Thomas
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - Allison R. Thompson
- Biology Department, Western Kentucky University, Bowling Green, Kentucky, United States of America
| | - Lorianna Vanderveen
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Rohan Varma
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Hannah L. Vaught
- Biology Department, University of Wisconsin-River Falls, River Falls, Wisconsin, United States of America
| | - Quynh D. Vo
- Department of Biological Sciences, University of North Texas, Denton, Texas, United States of America
| | - Zachary T. Vonberg
- Biology Department, University of Wisconsin-River Falls, River Falls, Wisconsin, United States of America
| | - Vassie C. Ware
- Biological Sciences, Lehigh University, Bethlehem, Pennsylvania, United States of America
| | - Yasmene M. Warrad
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - Kaitlyn E. Wathen
- Biology Department, Western Kentucky University, Bowling Green, Kentucky, United States of America
| | - Jonathan L. Weinstein
- Biology Department, Saint Joseph’s University, Philadelphia, Pennsylvania, United States of America
| | - Jacqueline F. Wyper
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - Jakob R. Yankauskas
- Biology Department, Bucknell University, Lewisburg, Pennsylvania, United States of America
| | - Christine Zhang
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Graham F. Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- * E-mail:
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90
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Barbour AG, Adeolu M, Gupta RS. Division of the genus Borrelia into two genera (corresponding to Lyme disease and relapsing fever groups) reflects their genetic and phenotypic distinctiveness and will lead to a better understanding of these two groups of microbes (Margos et al. (2016) There is inadequate evidence to support the division of the genus Borrelia. Int. J. Syst. Evol. Microbiol. doi: 10.1099/ijsem.0.001717). Int J Syst Evol Microbiol 2017; 67:2058-2067. [PMID: 28141502 DOI: 10.1099/ijsem.0.001815] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Alan G Barbour
- Departments of Medicine, Microbiology & Molecular Genetics, and Ecology & Evolutionary Biology, University of California, Irvine, California, USA
| | - Mobolaji Adeolu
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Radhey S Gupta
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
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91
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Gupta RS, Nanda A, Khadka B. Novel molecular, structural and evolutionary characteristics of the phosphoketolases from bifidobacteria and Coriobacteriales. PLoS One 2017; 12:e0172176. [PMID: 28212383 PMCID: PMC5315409 DOI: 10.1371/journal.pone.0172176] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 01/12/2017] [Indexed: 12/23/2022] Open
Abstract
Members from the order Bifidobacteriales, which include many species exhibiting health promoting effects, differ from all other organisms in using a unique pathway for carbohydrate metabolism, known as the "bifid shunt", which utilizes the enzyme phosphoketolase (PK) to carry out the phosphorolysis of both fructose-6-phosphate (F6P) and xylulose-5-phosphate (X5P). In contrast to bifidobacteria, the PKs found in other organisms (referred to XPK) are able to metabolize primarily X5P and show very little activity towards F6P. Presently, very little is known about the molecular or biochemical basis of the differences in the two forms of PKs. Comparative analyses of PK sequences from different organisms reported here have identified multiple high-specific sequence features in the forms of conserved signature inserts and deletions (CSIs) in the PK sequences that clearly distinguish the X5P/F6P phosphoketolases (XFPK) of bifidobacteria from the XPK homologs found in most other organisms. Interestingly, most of the molecular signatures that are specific for the XFPK from bifidobacteria are also shared by the PK homologs from the Coriobacteriales order of Actinobacteria. Similarly to the Bifidobacteriales, the order Coriobacteriales is also made up of commensal organisms, that are saccharolytic and able to metabolize wide variety of carbohydrates, producing lactate and other metabolites. Phylogenetic studies provide evidence that the XFPK from bifidobacteria are specifically related to those found in the Coriobacteriales and suggest that the gene for PK (XFPK) was horizontally transferred between these two groups. A number of the identified CSIs in the XFPK sequence, which serve to distinguish the XFPK homologs from XPK homologs, are located at the subunit interface in the structure of the XFPK dimer protein. The results of protein modelling and subunit docking studies indicate that these CSIs are involved in the formation/stabilization of the protein dimer. The significance of these observations regarding the differences in the activities of the XFPK and XPK homologs are discussed. Additionally, this work also discusses the significance of the XFPK-like homologs, similar to those found in bifidobacteria, in the order Coriobacteriales.
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Affiliation(s)
- Radhey S. Gupta
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Anish Nanda
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Bijendra Khadka
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
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92
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Paulus C, Rebets Y, Tokovenko B, Nadmid S, Terekhova LP, Myronovskyi M, Zotchev SB, Rückert C, Braig S, Zahler S, Kalinowski J, Luzhetskyy A. New natural products identified by combined genomics-metabolomics profiling of marine Streptomyces sp. MP131-18. Sci Rep 2017; 7:42382. [PMID: 28186197 PMCID: PMC5301196 DOI: 10.1038/srep42382] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2016] [Accepted: 01/10/2017] [Indexed: 01/13/2023] Open
Abstract
Marine actinobacteria are drawing more and more attention as a promising source of new natural products. Here we report isolation, genome sequencing and metabolic profiling of new strain Streptomyces sp. MP131-18 isolated from marine sediment sample collected in the Trondheim Fjord, Norway. The 16S rRNA and multilocus phylogenetic analysis showed that MP131-18 belongs to the genus Streptomyces. The genome of MP131-18 isolate was sequenced, and 36 gene clusters involved in the biosynthesis of 18 different types of secondary metabolites were predicted using antiSMASH analysis. The combined genomics-metabolics profiling of the strain led to the identification of several new biologically active compounds. As a result, the family of bisindole pyrroles spiroindimicins was extended with two new members, spiroindimicins E and F. Furthermore, prediction of the biosynthetic pathway for unusual α-pyrone lagunapyrone isolated from MP131-18 resulted in foresight and identification of two new compounds of this family – lagunapyrones D and E. The diversity of identified and predicted compounds from Streptomyces sp. MP131-18 demonstrates that marine-derived actinomycetes are not only a promising source of new natural products, but also represent a valuable pool of genes for combinatorial biosynthesis of secondary metabolites.
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Affiliation(s)
- Constanze Paulus
- Helmholtz-Institute for Pharmaceutical Research Saarland, Actinobacteria Metabolic Engineering Group, Saarbrücken, Germany
| | - Yuriy Rebets
- Helmholtz-Institute for Pharmaceutical Research Saarland, Actinobacteria Metabolic Engineering Group, Saarbrücken, Germany
| | - Bogdan Tokovenko
- Helmholtz-Institute for Pharmaceutical Research Saarland, Actinobacteria Metabolic Engineering Group, Saarbrücken, Germany
| | - Suvd Nadmid
- Helmholtz-Institute for Pharmaceutical Research Saarland, Actinobacteria Metabolic Engineering Group, Saarbrücken, Germany
| | - Larisa P Terekhova
- Gause Institute of New Antibiotics, Russian Academy of Medical Sciences, Moscow, Russia
| | - Maksym Myronovskyi
- Helmholtz-Institute for Pharmaceutical Research Saarland, Actinobacteria Metabolic Engineering Group, Saarbrücken, Germany
| | - Sergey B Zotchev
- Department of Biotechnology, Norwegian University of Science and Technology, Trondheim, Norway.,Department of Pharmacognosy, University of Vienna, Vienna, Austria
| | | | - Simone Braig
- Department of Pharmacy - Center for Drug Research, University of Munich, Munich, Germany
| | - Stefan Zahler
- Department of Pharmacy - Center for Drug Research, University of Munich, Munich, Germany
| | - Jörn Kalinowski
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Andriy Luzhetskyy
- Helmholtz-Institute for Pharmaceutical Research Saarland, Actinobacteria Metabolic Engineering Group, Saarbrücken, Germany.,Universität des Saarlandes, Pharmaceutical Biotechnology, Saarbrücken, Germany
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93
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Velsko IM, Overmyer KA, Speller C, Klaus L, Collins MJ, Loe L, Frantz LAF, Sankaranarayanan K, Lewis CM, Martinez JBR, Chaves E, Coon JJ, Larson G, Warinner C. The dental calculus metabolome in modern and historic samples. Metabolomics 2017; 13:134. [PMID: 29046620 PMCID: PMC5626792 DOI: 10.1007/s11306-017-1270-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 09/21/2017] [Indexed: 12/23/2022]
Abstract
INTRODUCTION Dental calculus is a mineralized microbial dental plaque biofilm that forms throughout life by precipitation of salivary calcium salts. Successive cycles of dental plaque growth and calcification make it an unusually well-preserved, long-term record of host-microbial interaction in the archaeological record. Recent studies have confirmed the survival of authentic ancient DNA and proteins within historic and prehistoric dental calculus, making it a promising substrate for investigating oral microbiome evolution via direct measurement and comparison of modern and ancient specimens. OBJECTIVE We present the first comprehensive characterization of the human dental calculus metabolome using a multi-platform approach. METHODS Ultra performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) quantified 285 metabolites in modern and historic (200 years old) dental calculus, including metabolites of drug and dietary origin. A subset of historic samples was additionally analyzed by high-resolution gas chromatography-MS (GC-MS) and UPLC-MS/MS for further characterization of metabolites and lipids. Metabolite profiles of modern and historic calculus were compared to identify patterns of persistence and loss. RESULTS Dipeptides, free amino acids, free nucleotides, and carbohydrates substantially decrease in abundance and ubiquity in archaeological samples, with some exceptions. Lipids generally persist, and saturated and mono-unsaturated medium and long chain fatty acids appear to be well-preserved, while metabolic derivatives related to oxidation and chemical degradation are found at higher levels in archaeological dental calculus than fresh samples. CONCLUSIONS The results of this study indicate that certain metabolite classes have higher potential for recovery over long time scales and may serve as appropriate targets for oral microbiome evolutionary studies.
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Affiliation(s)
- Irina M. Velsko
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford, OX1 3QY UK
- Present Address: Department of Biological Sciences, Clemson University, Clemson, SC 29634 USA
| | | | - Camilla Speller
- BioArCh, Department of Archaeology, University of York, York, YO10 5DD UK
| | - Lauren Klaus
- Department of Periodontics, University of Oklahoma Health Sciences Center, Oklahoma, OK USA
| | - Matthew J. Collins
- BioArCh, Department of Archaeology, University of York, York, YO10 5DD UK
- Museum of Natural History, University of Copenhagen, Copenhagen, Denmark
| | - Louise Loe
- Heritage Burial Services, Oxford Archaeology, Oxford, UK
| | - Laurent A. F. Frantz
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford, OX1 3QY UK
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS UK
| | | | - Cecil M. Lewis
- Department of Anthropology, University of Oklahoma, Norman, OK 73019 USA
| | | | - Eros Chaves
- Department of Periodontics, University of Oklahoma Health Sciences Center, Oklahoma, OK USA
- Present Address: Pinellas Dental Specialties, Largo, FL 33776 USA
| | - Joshua J. Coon
- Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI 53706 USA
- Departments of Chemistry and Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706 USA
- Morgridge Institute for Research, Madison, WI 53706 USA
| | - Greger Larson
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford, OX1 3QY UK
| | - Christina Warinner
- Department of Periodontics, University of Oklahoma Health Sciences Center, Oklahoma, OK USA
- Department of Anthropology, University of Oklahoma, Norman, OK 73019 USA
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07743 Jena, Germany
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94
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Bae KS, Kim MS, Lee JH, Kang JW, Kim DI, Lee JH, Seong CN. Korean indigenous bacterial species with valid names belonging to the phylum Actinobacteria. J Microbiol 2016; 54:789-795. [PMID: 27888457 DOI: 10.1007/s12275-016-6446-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 11/02/2016] [Indexed: 11/26/2022]
Abstract
To understand the isolation and classification state of actinobacterial species with valid names for Korean indigenous isolates, isolation source, regional origin, and taxonomic affiliation of the isolates were studied. At the time of this writing, the phylum Actinobacteria consisted of only one class, Actinobacteria, including five subclasses, 10 orders, 56 families, and 330 genera. Moreover, new taxa of this phylum continue to be discovered. Korean actinobacterial species with a valid name has been reported from 1995 as Tsukamurella inchonensis isolated from a clinical specimen. In 1997, Streptomyces seoulensis was validated with the isolate from the natural Korean environment. Until Feb. 2016, 256 actinobacterial species with valid names originated from Korean territory were listed on LPSN. The species were affiliated with three subclasses (Acidimicrobidae, Actinobacteridae, and Rubrobacteridae), four orders (Acidimicrobiales, Actinomycetales, Bifidobacteriales, and Solirubrobacterales), 12 suborders, 36 families, and 93 genera. Most of the species belonged to the subclass Actinobacteridae, and almost of the members of this subclass were affiliated with the order Actinomycetales. A number of novel isolates belonged to the families Nocardioidaceae, Microbacteriaceae, Intrasporangiaceae, and Streptomycetaceae as well as the genera Nocardioides, Streptomyces, and Microbacterium. Twenty-six novel genera and one novel family, Motilibacteraceae, were created first with Korean indigenous isolates. Most of the Korean indigenous actionobacterial species were isolated from natural environments such as soil, seawater, tidal flat sediment, and fresh-water. A considerable number of species were isolated from artificial resources such as fermented foods, wastewater, compost, biofilm, and water-cooling systems or clinical specimens. Korean indigenous actinobacterial species were isolated from whole territory of Korea, and especially a large number of species were from Jeju, Gyeonggi, Jeonnam, Daejeon, and Chungnam. A large number of novel actinobacterial species continue to be discovered since the Korean government is encouraging the search for new bacterial species and researchers are endeavoring to find out novel strains from extreme or untapped environments.
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Affiliation(s)
- Kyung Sook Bae
- Biological Resource Center, KRIBB, Jeongeup, 56212, Republic of Korea
| | - Mi Sun Kim
- Department of Biology, College of Life Science and Natural Resources, Sunchon National University, Suncheon, 57922, Republic of Korea
| | - Ji Hee Lee
- Department of Biology, College of Life Science and Natural Resources, Sunchon National University, Suncheon, 57922, Republic of Korea
| | - Joo Won Kang
- Department of Biology, College of Life Science and Natural Resources, Sunchon National University, Suncheon, 57922, Republic of Korea
| | - Dae In Kim
- Department of Biology, College of Life Science and Natural Resources, Sunchon National University, Suncheon, 57922, Republic of Korea
| | - Ji Hee Lee
- Department of Biology, College of Life Science and Natural Resources, Sunchon National University, Suncheon, 57922, Republic of Korea
| | - Chi Nam Seong
- Department of Biology, College of Life Science and Natural Resources, Sunchon National University, Suncheon, 57922, Republic of Korea.
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95
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Esposito LA, Gupta S, Streiter F, Prasad A, Dennehy JJ. Evolutionary interpretations of mycobacteriophage biodiversity and host-range through the analysis of codon usage bias. Microb Genom 2016; 2:e000079. [PMID: 28348827 PMCID: PMC5359403 DOI: 10.1099/mgen.0.000079] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 07/18/2016] [Indexed: 12/31/2022] Open
Abstract
In an genomics course sponsored by the Howard Hughes Medical Institute (HHMI), undergraduate students have isolated and sequenced the genomes of more than 1,150 mycobacteriophages, creating the largest database of sequenced bacteriophages able to infect a single host, Mycobacterium smegmatis, a soil bacterium. Genomic analysis indicates that these mycobacteriophages can be grouped into 26 clusters based on genetic similarity. These clusters span a continuum of genetic diversity, with extensive genomic mosaicism among phages in different clusters. However, little is known regarding the primary hosts of these mycobacteriophages in their natural habitats, nor of their broader host ranges. As such, it is possible that the primary host of many newly isolated mycobacteriophages is not M. smegmatis, but instead a range of closely related bacterial species. However, determining mycobacteriophage host range presents difficulties associated with mycobacterial cultivability, pathogenicity and growth. Another way to gain insight into mycobacteriophage host range and ecology is through bioinformatic analysis of their genomic sequences. To this end, we examined the correlations between the codon usage biases of 199 different mycobacteriophages and those of several fully sequenced mycobacterial species in order to gain insight into the natural host range of these mycobacteriophages. We find that UPGMA clustering tends to match, but not consistently, clustering by shared nucleotide sequence identify. In addition, analysis of GC content, tRNA usage and correlations between mycobacteriophage and mycobacterial codon usage bias suggests that the preferred host of many clustered mycobacteriophages is not M. smegmatis but other, as yet unknown, members of the mycobacteria complex or closely allied bacterial species.
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Affiliation(s)
| | - Swati Gupta
- Biology Department, Queens College, Queens, NY 11367, USA
| | | | - Ashley Prasad
- Biology Department, Queens College, Queens, NY 11367, USA
| | - John J. Dennehy
- Biology Department, Queens College, Queens, NY 11367, USA
- Biology PhD Program, The Graduate Center of the City University of New York, New York, NY 10016, USA
- Correspondence John J. Dennehy ()
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96
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Streptomyces caldifontis sp. nov., isolated from a hot water spring of Tatta Pani, Kotli, Pakistan. Antonie van Leeuwenhoek 2016; 110:77-86. [PMID: 27730318 DOI: 10.1007/s10482-016-0778-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 09/29/2016] [Indexed: 10/20/2022]
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97
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Kao WC, Kleinschroth T, Nitschke W, Baymann F, Neehaul Y, Hellwig P, Richers S, Vonck J, Bott M, Hunte C. The obligate respiratory supercomplex from Actinobacteria. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:1705-14. [PMID: 27472998 DOI: 10.1016/j.bbabio.2016.07.009] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 06/27/2016] [Accepted: 07/23/2016] [Indexed: 10/21/2022]
Abstract
Actinobacteria are closely linked to human life as industrial producers of bioactive molecules and as human pathogens. Respiratory cytochrome bcc complex and cytochrome aa3 oxidase are key components of their aerobic energy metabolism. They form a supercomplex in the actinobacterial species Corynebacterium glutamicum. With comprehensive bioinformatics and phylogenetic analysis we show that genes for cyt bcc-aa3 supercomplex are characteristic for Actinobacteria (Actinobacteria and Acidimicrobiia, except the anaerobic orders Actinomycetales and Bifidobacteriales). An obligatory supercomplex is likely, due to the lack of genes encoding alternative electron transfer partners such as mono-heme cyt c. Instead, subunit QcrC of bcc complex, here classified as short di-heme cyt c, will provide the exclusive electron transfer link between the complexes as in C. glutamicum. Purified to high homogeneity, the C. glutamicum bcc-aa3 supercomplex contained all subunits and cofactors as analyzed by SDS-PAGE, BN-PAGE, absorption and EPR spectroscopy. Highly uniform supercomplex particles in electron microscopy analysis support a distinct structural composition. The supercomplex possesses a dimeric stoichiometry with a ratio of a-type, b-type and c-type hemes close to 1:1:1. Redox titrations revealed a low potential bcc complex (Em(ISP)=+160mV, Em(bL)=-291mV, Em(bH)=-163mV, Em(cc)=+100mV) fined-tuned for oxidation of menaquinol and a mixed potential aa3 oxidase (Em(CuA)=+150mV, Em(a/a3)=+143/+317mV) mediating between low and high redox potential to accomplish dioxygen reduction. The generated molecular model supports a stable assembled supercomplex with defined architecture which permits energetically efficient coupling of menaquinol oxidation and dioxygen reduction in one supramolecular entity.
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Affiliation(s)
- Wei-Chun Kao
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, BIOSS Centre for Biological Signalling Studies, 79104 Freiburg, Germany
| | - Thomas Kleinschroth
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, BIOSS Centre for Biological Signalling Studies, 79104 Freiburg, Germany
| | - Wolfgang Nitschke
- Laboratoire de Bioénergétique et Ingénierie des Protéines UMR 7281 CNRS/Aix Marseille Univ, FR3479, 13009 Marseille, France
| | - Frauke Baymann
- Laboratoire de Bioénergétique et Ingénierie des Protéines UMR 7281 CNRS/Aix Marseille Univ, FR3479, 13009 Marseille, France
| | - Yashvin Neehaul
- Laboratoire de bioélectrochimie et spectroscopie, UMR 7140, Chimie de la matière complexe, CNRS-Université de Strasbourg, 1 rue Blaise Pascal, 67070 Strasbourg, France
| | - Petra Hellwig
- Laboratoire de bioélectrochimie et spectroscopie, UMR 7140, Chimie de la matière complexe, CNRS-Université de Strasbourg, 1 rue Blaise Pascal, 67070 Strasbourg, France
| | - Sebastian Richers
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
| | - Janet Vonck
- Department of Structural Biology, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
| | - Michael Bott
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, 52428 Jülich, Germany
| | - Carola Hunte
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, BIOSS Centre for Biological Signalling Studies, 79104 Freiburg, Germany.
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98
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Zhang G, Gao B, Adeolu M, Khadka B, Gupta RS. Phylogenomic Analyses and Comparative Studies on Genomes of the Bifidobacteriales: Identification of Molecular Signatures Specific for the Order Bifidobacteriales and Its Different Subclades. Front Microbiol 2016; 7:978. [PMID: 27446019 PMCID: PMC4921777 DOI: 10.3389/fmicb.2016.00978] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 06/07/2016] [Indexed: 11/24/2022] Open
Abstract
The order Bifidobacteriales comprises a diverse variety of species found in the gastrointestinal tract of humans and other animals, some of which are opportunistic pathogens, whereas a number of others exhibit health-promoting effects. However, currently very few biochemical or molecular characteristics are known which are specific for the order Bifidobacteriales, or specific clades within this order, which distinguish them from other bacteria. This study reports the results of detailed comparative genomic and phylogenetic studies on 62 genome-sequenced species/strains from the order Bifidobacteriales. In a robust phylogenetic tree for the Bifidobacteriales constructed based on 614 core proteins, a number of well-resolved clades were observed including a clade separating the Scarodvia-related genera (Scardovia clade) from the genera Bifidobacterium and Gardnerella, as well as a number of previously reported clusters of Bifidobacterium spp. In parallel, our comparative analyses of protein sequences from the Bifidobacteriales genomes have identified numerous molecular markers that are specific for this group of bacteria. Of these markers, 32 conserved signature indels (CSIs) in widely distributed proteins and 10 signature proteins are distinctive characteristics of all sequenced Bifidobacteriales species and provide novel and highly specific means for distinguishing these bacteria. In addition, multiple other molecular signatures are specific for the following clades of Bifidobacteriales: (i) 5 CSIs specific for a clade comprising of the Scardovia-related genera; (ii) 3 CSIs and 2 CSPs specific for a clade consisting of the Bifidobacterium and Gardnerella spp.; (iii) multiple other signatures demarcating a number of clusters of the B. asteroides-and B. longum- related species. The described molecular markers provide novel and reliable means for distinguishing the Bifidobacteriales and a number of their clades in molecular terms and for the classification of these bacteria. The Bifidobacteriales-specific CSIs, found in important proteins, are predicted to play important roles in modifying the cellular functions of the affected proteins. Hence, biochemical studies on the cellular functions of these CSIs could lead to discovery of novel characteristics of either all Bifidobacteriales, or specific groups of bacteria within this order. Some of the functions affected/modified by these genetic changes could also be important for the probiotic/pathogenic activities of the bifidobacteria.
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Affiliation(s)
- Grace Zhang
- Department of Biochemistry and Biomedical Sciences, McMaster University Hamilton, ON, Canada
| | - Beile Gao
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences Guangzhou, China
| | - Mobolaji Adeolu
- Department of Biochemistry and Biomedical Sciences, McMaster University Hamilton, ON, Canada
| | - Bijendra Khadka
- Department of Biochemistry and Biomedical Sciences, McMaster University Hamilton, ON, Canada
| | - Radhey S Gupta
- Department of Biochemistry and Biomedical Sciences, McMaster University Hamilton, ON, Canada
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99
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Gupta RS. Impact of genomics on the understanding of microbial evolution and classification: the importance of Darwin's views on classification. FEMS Microbiol Rev 2016; 40:520-53. [PMID: 27279642 DOI: 10.1093/femsre/fuw011] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/14/2016] [Indexed: 12/24/2022] Open
Abstract
Analyses of genome sequences, by some approaches, suggest that the widespread occurrence of horizontal gene transfers (HGTs) in prokaryotes disguises their evolutionary relationships and have led to questioning of the Darwinian model of evolution for prokaryotes. These inferences are critically examined in the light of comparative genome analysis, characteristic synapomorphies, phylogenetic trees and Darwin's views on examining evolutionary relationships. Genome sequences are enabling discovery of numerous molecular markers (synapomorphies) such as conserved signature indels (CSIs) and conserved signature proteins (CSPs), which are distinctive characteristics of different prokaryotic taxa. Based on these molecular markers, exhibiting high degree of specificity and predictive ability, numerous prokaryotic taxa of different ranks, currently identified based on the 16S rRNA gene trees, can now be reliably demarcated in molecular terms. Within all studied groups, multiple CSIs and CSPs have been identified for successive nested clades providing reliable information regarding their hierarchical relationships and these inferences are not affected by HGTs. These results strongly support Darwin's views on evolution and classification and supplement the current phylogenetic framework based on 16S rRNA in important respects. The identified molecular markers provide important means for developing novel diagnostics, therapeutics and for functional studies providing important insights regarding prokaryotic taxa.
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Affiliation(s)
- Radhey S Gupta
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
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100
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Alshaibani MM, Jalil J, Sidik NM, Edrada-Ebel R, Zin NM. Isolation and characterization of cyclo-(tryptophanyl-prolyl) and chloramphenicol from Streptomyces sp. SUK 25 with antimethicillin-resistant Staphylococcus aureus activity. DRUG DESIGN DEVELOPMENT AND THERAPY 2016; 10:1817-27. [PMID: 27330275 PMCID: PMC4896468 DOI: 10.2147/dddt.s101212] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Background Zingiber spectabile, commonly known as Beehive Ginger, is used as an ethnobotanical plant in many countries as an appetizer or to treat stomachache, toothache, muscle sprain, and as a cure for swelling, sores and cuts. This is the first report of isolation of Streptomyces strain from the root of this plant. Strain Universiti Kebangsaan 25 (SUK 25) has a very high activity to produce secondary metabolites against methicillin-resistant Staphylococcus aureus (MRSA), which is associated with high morbidity and mortality rates due to acquired multidrug resistance genes and causes medication failure in some clinical cases worldwide. Phylogenetic analysis based on the 16S ribosomal RNA gene sequence exhibited that the most closely related strain was Streptomyces omiyaensis NBRC 13449T (99.0% similarity). Aim This study was conducted to carry out the extraction, identification, and biological evaluation of active metabolites isolated from SUK 25 against three MRSA strains, namely, MRSA ATCC 43300, MRSA ATCC 33591, and MRSA ATCC 49476. Materials and methods The production of secondary metabolites by this strain was optimized through Thronton’s media. Isolation, purification, and identification of the bioactive compounds were carried out using reversed-phase high-performance liquid chromatography, high-resolution mass spectrometry, Fourier transform infrared, and one-dimensional and two-dimensional nuclear magnetic resonance. Results During screening procedure, SUK 25 exhibited good antimicrobial potential against several strains of MRSA. The best biological activity was shown from fraction number VII and its subfractions F2 and F3 with minimum inhibitory concentration values at 16 µg/mL and 8 µg/mL, respectively. These two subfractions were identified as diketopiperazine cyclo-(tryptophanyl-prolyl) and chloramphenicol. Conclusion On the basis of obtained results, SUK 25 isolated from Z. spectabile can be regarded as a new valuable source to produce secondary metabolites against bacteria, especially MRSA.
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Affiliation(s)
- Muhanna M Alshaibani
- Programme of Biomedical Science, School of Diagnostic and Applied Health Sciences, Faculty of Health Sciences, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Juriyati Jalil
- Drug and Herbal Research Centre, Faculty of Pharmacy, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Nik M Sidik
- School of Bioscience and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Malaysia
| | - Ruangelie Edrada-Ebel
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, Scotland
| | - Noraziah M Zin
- Programme of Biomedical Science, School of Diagnostic and Applied Health Sciences, Faculty of Health Sciences, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
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