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Gupta RS, Kanter-Eivin DA. AppIndels.com server: a web-based tool for the identification of known taxon-specific conserved signature indels in genome sequences. Validation of its usefulness by predicting the taxonomic affiliation of >700 unclassified strains of Bacillus species. Int J Syst Evol Microbiol 2023; 73. [PMID: 37159410 DOI: 10.1099/ijsem.0.005844] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023] Open
Abstract
Taxon-specific conserved signature indels (CSIs) in genes/proteins provide reliable molecular markers (synapomorphies) for unambiguous demarcation of taxa of different ranks in molecular terms and for genetic, biochemical and diagnostic studies. Because of their predictive abilities, the shared presence of known taxon-specific CSIs in genome sequences has proven useful for taxonomic purposes. However, the lack of a convenient method for identifying the presence of known CSIs in genome sequences has limited their utility for taxonomic and other studies. We describe here a web-based tool/server (AppIndels.com) that identifies the presence of known and validated CSIs in genome sequences and uses this information for predicting taxonomic affiliation. The utility of this server was tested by using a database of 585 validated CSIs, which included 350 CSIs specific for ≈45 Bacillales genera, with the remaining CSIs being specific for members of the orders Neisseriales, Legionellales and Chlorobiales, family Borreliaceae, and some Pseudomonadaceae species/genera. Using this server, genome sequences were analysed for 721 Bacillus strains of unknown taxonomic affiliation. Results obtained showed that 651 of these genomes contained significant numbers of CSIs specific for the following Bacillales genera/families: Alkalicoccus, 'Alkalihalobacillaceae', Alteribacter, Bacillus Cereus clade, Bacillus Subtilis clade, Caldalkalibacillus, Caldibacillus, Cytobacillus, Ferdinandcohnia, Gottfriedia, Heyndrickxia, Lederbergia, Litchfieldia, Margalitia, Mesobacillus, Metabacillus, Neobacillus, Niallia, Peribacillus, Priestia, Pseudalkalibacillus, Robertmurraya, Rossellomorea, Schinkia, Siminovitchia, Sporosarcina, Sutcliffiella, Weizmannia and Caryophanaceae. Validity of the taxon assignment made by the server was examined by reconstructing phylogenomic trees. In these trees, all Bacillus strains for which taxonomic predictions were made correctly branched with the indicated taxa. The unassigned strains likely correspond to taxa for which CSIs are lacking in our database. Results presented here show that the AppIndels server provides a useful new tool for predicting taxonomic affiliation based on shared presence of the taxon-specific CSIs. Some caveats in using this server are discussed.
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Affiliation(s)
- Radhey S Gupta
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario CA L8N 3Z5, Canada
| | - David A Kanter-Eivin
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario CA L8N 3Z5, Canada
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Yin D, Zhai F, Lu W, Moss AF, Kuang Y, Li F, Zhu Y, Zhang R, Zhang Y, Zhang S. Comparison of Coated and Uncoated Trace Minerals on Growth Performance, Tissue Mineral Deposition, and Intestinal Microbiota in Ducks. Front Microbiol 2022; 13:831945. [PMID: 35495727 PMCID: PMC9039745 DOI: 10.3389/fmicb.2022.831945] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 02/15/2022] [Indexed: 01/04/2023] Open
Abstract
Abnormally low or high levels of trace elements in poultry diets may elicit health problems associated with deficiency and toxicity, and impact poultry growth. The optimal supplement pattern of trace mineral also impacts the digestion and absorption in the body. For ducks, the limited knowledge of trace element requirements puzzled duck production. Thus, the objective of this study was to investigate the influence of dietary inclusions of coated and uncoated trace minerals on duck growth performance, tissue mineral deposition, serum antioxidant status, and intestinal microbiota profile. A total of 1,080 14-day-old Cherry Valley male ducks were randomly divided into six dietary treatment groups in a 2 (uncoated or coated trace minerals) × 3 (300, 500, or 1,000 mg/kg supplementation levels) factorial design. Each treatment was replicated 12 times (15 birds per replicate). Coated trace minerals significantly improved average daily gain (p < 0.05), increased Zn, Se, and Fe content of serum, liver, and muscle, increased serum antioxidant enzyme (p < 0.05) and decreased the excreta Fe, Zn, and Cu concentrations. Inclusions of 500 mg/kg of coated trace minerals had a similar effect on serum trace minerals and tissue metal ion deposition as the 1,000 mg/kg inorganic trace minerals. Higher concentrations of Lactobacillus, Sphaerochatea, Butyricimonas, and Enterococcus were found in birds fed with coated trace minerals. In conclusion, diets supplemented with coated trace minerals could reduce the risk of environmental contamination from excreted minerals without affecting performance. Furthermore, coated trace minerals may improve the bioavailability of metal ions and the colonization of probiotic microbiota to protect microbial barriers and maintain gut health.
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Affiliation(s)
- Dafei Yin
- College of Animal Husbandry and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Feng Zhai
- Yichun Tequ Feed Company, Yichun, China
| | - Wenbiao Lu
- Fujian Syno Biotech Co., Ltd., Fuzhou, China
| | - Amy F Moss
- School of Environmental and Rural Science, University of New England, Armidale, NSW, Australia
| | | | - Fangfang Li
- College of Animal Husbandry and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Yujing Zhu
- College of Animal Husbandry and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Ruiyang Zhang
- College of Animal Husbandry and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Yong Zhang
- College of Animal Husbandry and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Shuyi Zhang
- College of Animal Husbandry and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
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3
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Gupta RS, Suggett C. Conserved Signatures in Protein Sequences Reliably Demarcate Different Clades of Rodents/Glires Species and Consolidate Their Evolutionary Relationships. Genes (Basel) 2022; 13:genes13020288. [PMID: 35205335 PMCID: PMC8871558 DOI: 10.3390/genes13020288] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Revised: 01/25/2022] [Accepted: 01/28/2022] [Indexed: 01/18/2023] Open
Abstract
The grandorder Glires, consisting of the orders Rodentia and Lagomorpha, encompasses a significant portion of the extant mammalian species including Rat, Mouse, Squirrel, Guinea pig and Beaver. Glires species play an important role in the ecosystem and provide valuable animal models for genetic studies and animal testing. Thus, it is important to reliably determine their evolutionary relationships and identify molecular characteristics that are specific for different species groups within the Glires. In this work, we have constructed a phylogenetic tree for >30 genome sequenced Glires species based on concatenated sequences of 25 conserved proteins. In this tree, members of different orders, suborders, and families within Glires formed strongly supported clades, and their interrelationships were also generally reliably resolved. In parallel, we conducted comparative analyses on more than 1500 protein sequences from Glires species to identify highly conserved molecular markers. These markers were comprised of conserved signature indels (CSIs) in proteins, which are specific for different Rodentia/Glires clades. Of the 41 novel CSIs identified in this work, some are specific for the entire Glires, Rodentia, or Lagomorpha clades, whereas many others reliably demarcate different family/suborder level clades of Rodentia (viz. Myomorpha, Castorimorpha, Sciuromorpha, Hystricomorpha, and Muroidea). Additionally, some of the CSIs also provide information regarding the interrelationships among Rodentia subgroups. Our analysis has also identified one CSI that is commonly shared by the Glires and Scandentia species (tree shrew), however, its evolutionary significance is unclear. Several of the identifed rodents-specific CSIs are present in conserved disease-related proteins. Thus, they provide novel molecular markers for genetic and biochemical studies on the functions of these proteins.
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Abstract
Sialic acids are present in humans and other metazoans, playing essential roles in physiological and pathological processes. Commensal and pathogenic bacteria have evolved the capacity to utilize sialic acids as nutrient and energy sources. However, in some actinobacteria, sialic acid catabolism (SAC) is associated with free-living populations. To unravel the distribution and evolutionary history of SAC in the phylum Actinobacteria, we analyzed the presence and diversity of the putative SAC gene cluster (nan) in 7,180 high-quality, nonredundant actinobacterial genomes that covered 1,969 species. The results showed that ∼13% of actinobacterial species had the potential to utilize sialic acids, with 45 species capable of anhydro-SAC, all except two of them through the canonical pathway. These species belonged to 20 orders and 81 genera, with ∼36% of them from four genera, Actinomyces, Bifidobacterium, Corynebacterium, and Streptomyces. Moreover, ∼40% of the nan-positive species are free living. Phylogenetic analysis of the key nan genes, nanA, nanK, and nanE, revealed a strong signal of horizontal gene transfer (HGT), accompanied with vertical inheritance and gene loss. This evolutionary pattern led to high diversity and differential distribution of nan among actinobacterial taxa and might cause the cluster to spread to some free-living species while losing in some host-associated species. The evolution of SAC in actinobacteria probably represents the evolution of certain kinds of noncore bacterial functions for environmental adaptation and lifestyle switch, in which HGT plays a dominant role. IMPORTANCE Sialic acids play essential roles in the physiology of humans and other metazoan animals, and microbial sialic acid catabolism (SAC) is one of the processes critical for pathogenesis. To date, microbial SAC is studied mainly in commensals and pathogens, while its distribution in free-living microbes and evolutionary pathway remain largely unexplored. Here, by examining all actinobacterial genomes available, we demonstrate that putative SAC is present in a small proportion of actinobacterial species, of which, however, ∼40% are free-living species. We also reveal remarkable difference in the distribution of SAC among actinobacterial taxa and high diversity of the putative SAC gene clusters. HGT plays a significant role in the evolution of SAC, accompanied with vertical inheritance and gene loss. Our results provide a comprehensive and systematic picture of the distribution and evolutionary history of SAC in actinobacteria, expanding the current knowledge on bacterial adaptation and diversification.
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Hanifi GR, Samadi Kafil H, Tayebi Khosroshahi H, Shapouri R, Asgharzadeh M. Bifidobacteriaceae Family Diversity in Gut Microbiota of Patients with Renal Failure. ARCHIVES OF RAZI INSTITUTE 2021; 76:521-528. [PMID: 34824745 PMCID: PMC8605840 DOI: 10.22092/ari.2020.352271.1557] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Accepted: 10/27/2020] [Indexed: 12/23/2022]
Abstract
Bifidobacteriaceae family are gut microbiota that exhibit probiotic or health promoting effects on the host. Several studies have suggested that gut microbiota are quantitatively and qualitatively altered in patients with chronic kidney disease (CKD) and end-stage renal disease (ESRD). The present study aimed to assess the members of Bifidobacteriaceae family in fecal samples of patients with CKD and ESRD and compare them with non-CKD/ESRD patients to find any changes in their counts and diversions in these patients. Twenty fresh fecal samples from patients with CKD/ESRD and twenty from non-CKD/ESRD patients were examined. Whole DNA was extracted from fecal samples and the gut microbiota composition was analyzed by next generation sequencing (NGS). A total of 651 strains were identified from 40 fecal samples, 8 (1.23%) strains of which were identified as family Bifidobacteriaceae. The most abundant species in both control and disease groups were Bifidobacterium adolescentis and Bifidobacterium longum subsp. longum, and the least abundant species in the disease group was Bifidobacterium animalis subsp. lactis. There was no significant difference in the abundance of various species between the disease and control groups (p < 0.05). This study confirms that the members of the Bifidobacteriaceae family are not altered in patients with CKD/ESRD.
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Affiliation(s)
- Gh. R Hanifi
- Department of Microbiology, Zanjan Branch, Islamic Azad University, Zanjan, Iran
| | - H Samadi Kafil
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - R Shapouri
- Department of Microbiology, Zanjan Branch, Islamic Azad University, Zanjan, Iran
| | - M Asgharzadeh
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
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Li Y, Wang M, Sun ZZ, Xie BB. Comparative Genomic Insights Into the Taxonomic Classification, Diversity, and Secondary Metabolic Potentials of Kitasatospora, a Genus Closely Related to Streptomyces. Front Microbiol 2021; 12:683814. [PMID: 34194415 PMCID: PMC8236941 DOI: 10.3389/fmicb.2021.683814] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 05/20/2021] [Indexed: 11/25/2022] Open
Abstract
While the genus Streptomyces (family Streptomycetaceae) has been studied as a model for bacterial secondary metabolism and genetics, its close relatives have been less studied. The genus Kitasatospora is the second largest genus in the family Streptomycetaceae. However, its taxonomic position within the family remains under debate and the secondary metabolic potential remains largely unclear. Here, we performed systematic comparative genomic and phylogenomic analyses of Kitasatospora. Firstly, the three genera within the family Streptomycetaceae (Kitasatospora, Streptomyces, and Streptacidiphilus) showed common genomic features, including high G + C contents, high secondary metabolic potentials, and high recombination frequencies. Secondly, phylogenomic and comparative genomic analyses revealed phylogenetic distinctions and genome content differences among these three genera, supporting Kitasatospora as a separate genus within the family. Lastly, the pan-genome analysis revealed extensive genetic diversity within the genus Kitasatospora, while functional annotation and genome content comparison suggested genomic differentiation among lineages. This study provided new insights into genomic characteristics of the genus Kitasatospora, and also uncovered its previously underestimated and complex secondary metabolism.
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Affiliation(s)
- Yisong Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Meng Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Zhong-Zhi Sun
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Bin-Bin Xie
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
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Almada-Érix CN, Almada CN, Cabral L, Barros de Medeiros VP, Roquetto AR, Santos-Junior VA, Fontes M, Gonçalves AESS, Dos Santos A, Lollo PC, Magnani M, Sant'Ana AS. Orange Juice and Yogurt Carrying Probiotic Bacillus coagulans GBI-30 6086: Impact of Intake on Wistar Male Rats Health Parameters and Gut Bacterial Diversity. Front Microbiol 2021; 12:623951. [PMID: 34135869 PMCID: PMC8202523 DOI: 10.3389/fmicb.2021.623951] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 03/03/2021] [Indexed: 01/14/2023] Open
Abstract
This study aimed to investigate the impact of the food matrix (orange juice and yogurt) on the effects of the spore-forming probiotic microorganism Bacillus coagulans GBI-30 6086 in health parameters and gastrointestinal tract (gut) bacterial diversity in Wistar male rats. Rats (n = 48) were randomly distributed into six groups. The groups were the Control (which received sterile distilled water), Juice (which received orange juice), Yogurt (which received yogurt), Probiotic Bacillus (which received B. coagulans GBI-30 6086 in distilled water), Probiotic Juice (which received orange juice with B. coagulans GBI-30 6086), and Probiotic Yogurt (which received yogurt with B. coagulans GBI-30 6086). Each animal belonging to the different groups was treated for 21 days. The daily administration of probiotic juice or probiotic yogurt did not affect the rats’ food or body weight. Rats fed with Probiotic Yogurt showed lower glucose and triglycerides levels (p < 0.05) in comparison to the control group (p < 0.05), while no changes in these parameters were observed in the rats fed with Probiotic Juice. Rats fed with Probiotic Yogurt showed a higher gut bacterial diversity than the control group (p < 0.05), and higher abundance (p < 0.05) of Vibrionales, Enterobacteriales, Burkholderiales, Erysipelotrichales, and Bifidobacteriales compared to all other groups. No changes were observed in the expression levels of antioxidant enzymes or heat shock protein 70 of rats fed with probiotic yogurt or probiotic juice. Results reveal that the consumption of yogurt containing B. coagulans GBI-30 6086 decreases triglycerides and glucose levels and positively impacts the gut bacterial ecology in healthy rats. These animal model findings indicate that the matrix also impacts the functionality of foods carrying spore-forming probiotics. Besides, this research indicates that yogurt is also a suitable food carrier of Bacillus coagulans GBI-30 6086.
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Affiliation(s)
- Carine N Almada-Érix
- Department of Food Science and Nutrition, Faculty of Food Engineering, University of Campinas, Campinas, Brazil
| | - Caroline N Almada
- Department of Food Science and Nutrition, Faculty of Food Engineering, University of Campinas, Campinas, Brazil
| | - Lucélia Cabral
- Institute of Biosciences, Department of General and Applied Biology, São Paulo State University (UNESP), Rio Claro, Brazil
| | - Viviane Priscila Barros de Medeiros
- Laboratory of Microbial Processes in Food, Department of Food Engineering, Technology Center, Federal University of Paraíba, João Pessoa, Brazil
| | - Aline R Roquetto
- Department of Food Science and Nutrition, Faculty of Food Engineering, University of Campinas, Campinas, Brazil
| | - Valfredo A Santos-Junior
- Department of Food Science and Nutrition, Faculty of Food Engineering, University of Campinas, Campinas, Brazil.,Department of Physical Education, Federal University of Great Dourados, Dourados, Brazil
| | - Melline Fontes
- Research Informatics Core, Research Resource Center, University of Illinois at Chicago, Chicago, IL, United States.,Microbial Resources Division, Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas, Campinas, Brazil
| | - Any Elisa S S Gonçalves
- Internal Medicine Department, Faculty of Medical Sciences, University of Campinas, Campinas, Brazil
| | - Andrey Dos Santos
- Internal Medicine Department, Faculty of Medical Sciences, University of Campinas, Campinas, Brazil
| | - Pablo C Lollo
- Department of Food Science and Nutrition, Faculty of Food Engineering, University of Campinas, Campinas, Brazil.,Department of Physical Education, Federal University of Great Dourados, Dourados, Brazil
| | - Marciane Magnani
- Laboratory of Microbial Processes in Food, Department of Food Engineering, Technology Center, Federal University of Paraíba, João Pessoa, Brazil
| | - Anderson S Sant'Ana
- Department of Food Science and Nutrition, Faculty of Food Engineering, University of Campinas, Campinas, Brazil
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Duranti S, Lugli GA, Viappiani A, Mancabelli L, Alessandri G, Anzalone R, Longhi G, Milani C, Ossiprandi MC, Turroni F, Ventura M. Characterization of the phylogenetic diversity of two novel species belonging to the genus Bifidobacterium: Bifidobacterium cebidarum sp. nov. and Bifidobacterium leontopitheci sp. nov. Int J Syst Evol Microbiol 2020; 70:2288-2297. [PMID: 32065574 DOI: 10.1099/ijsem.0.004032] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Two Bifidobacterium strains, i.e., 2176BT and 2177BT, were isolated from Golden-Headed Lion Tamarin (Leontopithecus chrysomelas) and Goeldi's monkey (Callimico goeldii). Isolates were shown to be Gram-positive, non-motile, non-sporulating, facultative anaerobic and d-fructose 6-phosphate phosphoketolase-positive. Phylogenetic analyses based on 16S rRNA sequences, multilocus sequences (including hsp60, rpoB, dnaJ, dnaG and clpC genes) and the core genome revealed that bifidobacterial strains 2176BT and 2177BT exhibit close phylogenetic relatedness to Bifidobacterium felsineum DSM 103139T and Bifidobacterium bifidum LMG 11041T, respectively. Further genotyping based on the genome sequence of the isolated strains combined with phenotypic analyses, clearly show that these strains are distinct from each of the type strains of the so far recognized Bifidobacterium species. Thus, Bifidobacterium cebidarum sp. nov. (2176BT=LMG 31469T=CCUG 73785T) and Bifidobacterium leontopitheci sp. nov. (2177BT=LMG 31471T=CCUG 73786T are proposed as novel Bifidobacterium species.
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Affiliation(s)
- Sabrina Duranti
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | | | - Leonardo Mancabelli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | | | | | | | - Christian Milani
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | | | - Francesca Turroni
- Microbiome Research Hub, University of Parma, Parma, Italy.,Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy.,Microbiome Research Hub, University of Parma, Parma, Italy
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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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Zhang J, Bi JJ, Guo GJ, Yang L, Zhu B, Zhan GF, Li S, Huang NN, Hashimoto K, Yang C, Luo AL. Abnormal composition of gut microbiota contributes to delirium-like behaviors after abdominal surgery in mice. CNS Neurosci Ther 2019; 25:685-696. [PMID: 30680947 PMCID: PMC6515708 DOI: 10.1111/cns.13103] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 12/02/2018] [Accepted: 12/22/2018] [Indexed: 01/12/2023] Open
Abstract
Aims Anesthesia and surgery can cause delirium‐like symptoms postoperatively. Increasing evidence suggests that gut microbiota is a physiological regulator of the brain. Herein, we investigated whether gut microbiota plays a role in postoperative delirium (POD). Methods Mice were separated into non‐POD and POD phenotypes after abdominal surgery by applying hierarchical clustering analysis to behavioral tests. Fecal samples were collected, and 16S ribosomal RNA gene sequencing was performed to detect differences in gut microbiota composition among sham, non‐POD, and POD mice. Fecal bacteria from non‐POD and POD mice were transplanted into antibiotics‐induced pseudo‐germ‐free mice to investigate the effects on behaviors. Results α‐diversity and β‐diversity indicated differences in gut microbiota composition between the non‐POD and POD mice. At the phylum level, the non‐POD mice had significantly higher levels of Tenericutes, which were not detected in the POD mice. At the class level, levels of Gammaproteobacteria were higher in the POD mice, whereas the non‐POD mice had significantly higher levels of Mollicutes, which were not detected in the POD mice. A total of 20 gut bacteria differed significantly between the POD and non‐POD mice. Interestingly, the pseudo‐germ‐free mice showed abnormal behaviors prior to transplant. The pseudo‐germ‐free mice that received fecal bacteria transplants from non‐POD mice but not from POD mice showed improvements in behaviors. Conclusions Abnormal gut microbiota composition after abdominal surgery may contribute to the development of POD. A therapeutic strategy that targets gut microbiota could provide a novel alterative for POD treatment.
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Affiliation(s)
- Jie Zhang
- Department of Anesthesiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiang-Jiang Bi
- Department of Anesthesiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Guo-Jun Guo
- Department of Hand Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ling Yang
- Department of Cardiology and Critical Care Medicine, The Third Affiliated Hospital of Soochow University, Changzhou, China
| | - Bin Zhu
- Department of Cardiology and Critical Care Medicine, The Third Affiliated Hospital of Soochow University, Changzhou, China
| | - Gao-Feng Zhan
- Department of Anesthesiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shan Li
- Department of Anesthesiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Nian-Nian Huang
- Department of Anesthesiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Kenji Hashimoto
- Division of Clinical Neuroscience, Chiba University Center for Forensic Mental Health, Chiba, Japan
| | - Chun Yang
- Department of Anesthesiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ai-Lin Luo
- Department of Anesthesiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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11
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Vaneechoutte M, Guschin A, Van Simaey L, Gansemans Y, Van Nieuwerburgh F, Cools P. Emended description of Gardnerella vaginalis and description of Gardnerella leopoldii sp. nov., Gardnerella piotii sp. nov. and Gardnerella swidsinskii sp. nov., with delineation of 13 genomic species within the genus Gardnerella. Int J Syst Evol Microbiol 2019; 69:679-687. [PMID: 30648938 DOI: 10.1099/ijsem.0.003200] [Citation(s) in RCA: 107] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Whole genome sequence analysis (digital DNA-DNA hybridization and average nucleotide identity) was carried out for 81 sequenced full genomes of the genus Gardnerella, including ten determined in this study, and indicated the existence of 13 genomic species, of which five consist of only one strain and of which only five contain more than four sequenced genomes. Furthermore, a collection of ten Gardnerella strains, representing the emended species G. vaginalis and the newly described species Gardnerella leopoldii, Gardnerella piotii and Gardnerella swidsinskii, was studied. Matrix-assisted laser desorption ionization time-of-flight MS analysis of the protein signatures identified specific peaks that can be used to differentiate these four species. Only strains of G. vaginalis produce β-galactosidase. We emend the description of G. vaginalis (type strain ATCC 14018T=LMG 7832T=CCUG 3717T) and describe the novel species Gardnerella leopoldii sp. nov. (UGent 06.41T=LMG 30814T=CCUG 72425T), Gardnerella piotii sp. nov. (UGent 18.01T=LMG 30818T=CCUG 72427T) and Gardnerella swidsinskii sp. nov. (GS 9838-1T=LMG 30812T=CCUG 72429T).
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Affiliation(s)
- Mario Vaneechoutte
- 1Laboratory Bacteriology Research, Department of Diagnostic Sciences, Faculty of Medicine & Health Sciences, Ghent University, Flanders, Belgium
| | - Alexander Guschin
- 2Laboratory of Molecular Diagnostics and Epidemiology of Central Research Institute of Epidemiology, Moscow, Russia
| | - Leen Van Simaey
- 1Laboratory Bacteriology Research, Department of Diagnostic Sciences, Faculty of Medicine & Health Sciences, Ghent University, Flanders, Belgium
| | - Yannick Gansemans
- 3Laboratory of Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium
| | | | - Piet Cools
- 4Laboratory of Parasitology, Department of Virology, Parasitology and Immunology, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
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12
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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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13
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Killer J, Mekadim C, Pechar R, Bunešová V, Mrázek J, Vlková E. Gene encoding the CTP synthetase as an appropriate molecular tool for identification and phylogenetic study of the family Bifidobacteriaceae. Microbiologyopen 2018; 7:e00579. [PMID: 29356451 PMCID: PMC6079163 DOI: 10.1002/mbo3.579] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 12/04/2017] [Accepted: 12/07/2017] [Indexed: 02/02/2023] Open
Abstract
An alternative molecular marker with respect to the 16S rRNA gene demonstrating better identification and phylogenetic parameters has not been designed for the whole Bifidobacteriaceae family, which includes the genus Bifidobacterium and scardovial genera. Therefore, the aim of the study was to find such a gene in available genomic sequences, suggest appropriate means and conditions for asmplification and sequencing of the desired region of the selected gene in various strains of the bacterial family and verify the importance in classification and phylogeny. Specific primers flanking the variable region (~800 pb) within the pyrG gene encoding the CTP synthetase were designed by means of gene sequences retrieved from the genomes of strains belonging to the family Bifidobacteriaceae. The functionality and specificity of the primers were subsequently tested on the wild (7) and type strains of bifidobacteria (36) and scardovia (7). Comparative and phylogenetic studies based on obtained sequences revealed actual significance in classification and phylogeny of the Bifidobacteriaceae family. Gene statistics (percentages of mean sequence similarities and identical sites, mean number of nucleotide differences, P- and K-distances) and phylogenetic analyses (congruence between tree topologies, percentages of bootstrap values >50 and 70%) indicate that the pyrG gene represents an alternative identification and phylogenetic marker exhibiting higher discriminatory power among strains, (sub)species, and genera than the 16S rRNA gene. Sequences of the particular gene fragment, simply achieved through specific primers, enable more precisely to classify and evaluate phylogeny of the family Bifidobacteriaceae including, with some exceptions, health-promoting probiotic bacteria.
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Affiliation(s)
- Jiří Killer
- Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Prague 4 - Krč, Czechia.,Faculty of Agrobiology, Food and Natural Resources, Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Prague 6 - Suchdol, Czechia
| | - Chahrazed Mekadim
- Faculty of Agrobiology, Food and Natural Resources, Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Prague 6 - Suchdol, Czechia
| | - Radko Pechar
- Faculty of Agrobiology, Food and Natural Resources, Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Prague 6 - Suchdol, Czechia
| | - Věra Bunešová
- Faculty of Agrobiology, Food and Natural Resources, Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Prague 6 - Suchdol, Czechia
| | - Jakub Mrázek
- Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Prague 4 - Krč, Czechia
| | - Eva Vlková
- Faculty of Agrobiology, Food and Natural Resources, Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Prague 6 - Suchdol, Czechia
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14
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Duranti S, Mangifesta M, Lugli GA, Turroni F, Anzalone R, Milani C, Mancabelli L, Ossiprandi MC, Ventura M. Bifidobacterium vansinderenii sp. nov., isolated from faeces of emperor tamarin (Saguinus imperator). Int J Syst Evol Microbiol 2017; 67:3987-3995. [DOI: 10.1099/ijsem.0.002243] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Sabrina Duranti
- Department of Chemistry, Laboratory of Probiogenomics, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Marta Mangifesta
- Department of Chemistry, Laboratory of Probiogenomics, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
- GenProbio srl, Parma, Italy
| | - Gabriele Andrea Lugli
- Department of Chemistry, Laboratory of Probiogenomics, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Francesca Turroni
- Department of Chemistry, Laboratory of Probiogenomics, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Rosaria Anzalone
- Department of Chemistry, Laboratory of Probiogenomics, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Christian Milani
- Department of Chemistry, Laboratory of Probiogenomics, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Leonardo Mancabelli
- Department of Chemistry, Laboratory of Probiogenomics, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | | | - Marco Ventura
- Department of Chemistry, Laboratory of Probiogenomics, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
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15
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Gupta RS, Epand RM. Phylogenetic analysis of the diacylglycerol kinase family of proteins and identification of multiple highly-specific conserved inserts and deletions within the catalytic domain that are distinctive characteristics of different classes of DGK homologs. PLoS One 2017; 12:e0182758. [PMID: 28829789 PMCID: PMC5567653 DOI: 10.1371/journal.pone.0182758] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 07/24/2017] [Indexed: 01/01/2023] Open
Abstract
Diacylglycerol kinase (DGK) family of proteins, which phosphorylates diacylglycerol into phosphatidic acid, play important role in controlling diverse cellular processes in eukaryotic organisms. Most vertebrate species contain 10 different DGK isozymes, which are grouped into 5 different classes based on the presence or absence of specific functional domains. However, the relationships among different DGK isozymes or how they have evolved from a common ancestor is unclear. The catalytic domain constitutes the single largest sequence element within the DGK proteins that is commonly and uniquely shared by all family members, but there is limited understanding of the overall function of this domain. In this work, we have used the catalytic domain sequences to construct a phylogenetic tree for the DGK family members from representatives of the main vertebrate classes and have also examined the distributions of various DGK isozymes in eukaryotic phyla. In a tree based on catalytic domain sequences, the DGK homologs belonging to different classes formed strongly supported clusters which were separated by long branches, and the different isozymes within each class also generally formed monophyletic groupings. Further, our analysis of the sequence alignments of catalytic domains has identified >10 novel sequence signatures consisting of conserved signature indels (inserts or deletions, CSIs) that are distinctive characteristics of either particular classes of DGK isozymes, or are commonly shared by members of two or more classes of DGK isozymes. The conserved indels in protein sequences are known to play important functional roles in the proteins/organisms where they are found. Thus, our identification of multiple highly specific CSIs that are distinguishing characteristics of different classes of DGK homologs points to the existence of important differences in the catalytic domain function among the DGK isozymes. The identified CSIs in conjunction with the results of blast searches on species distribution of DGK isozymes also provide useful insights into the evolutionary relationships among the DGK family of proteins.
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Affiliation(s)
- Radhey S. Gupta
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
- * E-mail:
| | - Richard M. Epand
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
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16
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Lugli GA, Milani C, Turroni F, Duranti S, Mancabelli L, Mangifesta M, Ferrario C, Modesto M, Mattarelli P, Jiří K, van Sinderen D, Ventura M. Comparative genomic and phylogenomic analyses of the Bifidobacteriaceae family. BMC Genomics 2017; 18:568. [PMID: 28764658 PMCID: PMC5540593 DOI: 10.1186/s12864-017-3955-4] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 07/24/2017] [Indexed: 11/26/2022] Open
Abstract
Background Members of the Bifidobacteriaceae family represent both dominant microbial groups that colonize the gut of various animals, especially during the suckling stage of their life, while they also occur as pathogenic bacteria of the urogenital tract. The pan-genome of the genus Bifidobacterium has been explored in detail in recent years, though genomics of the Bifidobacteriaceae family has not yet received much attention. Here, a comparative genomic analyses of 67 Bifidobacteriaceae (sub) species including all currently recognized genera of this family, i.e., Aeriscardovia, Alloscardovia, Bifidobacterium, Bombiscardovia, Gardnerella, Neoscardovia, Parascardovia, Pseudoscardovia and Scardovia, was performed. Furthermore, in order to include a representative of each of the 67 (currently recognized) (sub) species belonging to the Bifidobacteriaceae family, we sequenced the genomes of an additional 11 species from this family, accomplishing the most extensive comparative genomic analysis performed within this family so far. Results Phylogenomics-based analyses revealed the deduced evolutionary pathway followed by each member of the Bifidobacteriaceae family, highlighting Aeriscardovia aeriphila LMG 21773 as the deepest branch in the evolutionary tree of this family. Furthermore, functional analyses based on genome content unveil connections between a given member of the family, its carbohydrate utilization abilities and its corresponding host. In this context, bifidobacterial (sub) species isolated from humans and monkeys possess the highest relative number of acquired glycosyl hydrolase-encoding genes, probably in order to enhance their metabolic ability to utilize different carbon sources consumed by the host. Conclusions Within the Bifidobacteriaceae family, genomics of the genus Bifidobacterium has been extensively investigated. In contrast, very little is known about the genomics of members of the other eight genera of this family. In this study, we decoded the genome sequences of each member of the Bifidobacteriaceae family. Thanks to subsequent comparative genomic and phylogenetic analyses, the deduced pan-genome of this family, as well as the predicted evolutionary development of each taxon belonging to this family was assessed. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3955-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Sabrina Duranti
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Leonardo Mancabelli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | | | - Chiara Ferrario
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Monica Modesto
- Department of Agricultural Sciences, University of Bologna, Bologna, Italy
| | - Paola Mattarelli
- Department of Agricultural Sciences, University of Bologna, Bologna, Italy
| | - Killer Jiří
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague, Czech Republic.,Institute of Animal Physiology and Genetics v.v.i., Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Douwe van Sinderen
- APC Microbiome Institute and School of Microbiology, National University of Ireland, Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy.
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17
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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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18
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Romkina AY, Kiriukhin MY. Biochemical and molecular characterization of the isocitrate dehydrogenase with dual coenzyme specificity from the obligate methylotroph Methylobacillus Flagellatus. PLoS One 2017; 12:e0176056. [PMID: 28423051 PMCID: PMC5397045 DOI: 10.1371/journal.pone.0176056] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 04/04/2017] [Indexed: 12/16/2022] Open
Abstract
The isocitrate dehydrogenase (MfIDH) with unique double coenzyme specificity from Methylobacillus flagellatus was purified and characterized, and its gene was cloned and overexpressed in E. coli as a fused protein. This enzyme is homodimeric,—with a subunit molecular mass of 45 kDa and a specific activity of 182 U mg -1 with NAD+ and 63 U mg -1 with NADP+. The MfIDH activity was dependent on divalent cations and Mn2+ enhanced the activity the most effectively. MfIDH exhibited a cofactor-dependent pH-activity profile. The optimum pH values were 8.5 (NAD+) and 6.0 (NADP+).The Km values for NAD+ and NADP+ were 113 μM and 184 μM respectively, while the Km values for DL-isocitrate were 9.0 μM (NAD+), 8.0 μM (NADP+). The MfIDH specificity (kcat/Km) was only 5-times higher for NAD+ than for NADP+. The purified MfIDH displayed maximal activity at 60°C. Heat-inactivation studies showed that the MfIDH was remarkably thermostable, retaining full activity at 50°C and losting ca. 50% of its activity after one hour of incubation at 75°C. The enzyme was insensitive to the presence of intermediate metabolites, with the exception of 2 mM ATP, which caused 50% inhibition of NADP+-linked activity. The indispensability of the N6 amino group of NAD(P)+ in its binding to MfIDH was demonstrated. MfIDH showed high sequence similarity with bacterial NAD(P)+-dependent type I isocitrate dehydrogenases (IDHs) rather than with eukaryotic NAD+-dependent IDHs. The unique double coenzyme specificity of MfIDH potentially resulted from the Lys340, Ile341 and Ala347 residues in the coenzyme-binding site of the enzyme. The discovery of a type I IDH with double coenzyme specificity elucidates the evolution of this subfamily IDHs and may provide fundamental information for engineering enzymes with desired properties.
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19
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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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