scholarly journals Molecular docking, dynamics and free energy analyses of Acinetobacter baumannii OXA class enzymes with carbapenems investigating their hydrolytic mechanisms

2020 ◽  
Vol 69 (8) ◽  
pp. 1062-1078
Author(s):  
Balajee Ramachandran ◽  
Jeyaraman Jeyakanthan ◽  
Bruno S. Lopes
Keyword(s):  
Free Energy ◽  
Acinetobacter Baumannii ◽  
Type Species ◽  
Three Dimensional ◽  
World Health ◽  
Phenotypic Data ◽  
Content Type ◽  
Beta Lactamases ◽  
Link Type ◽  
Class D

Introduction. Acinetobacter baumannii is a critical priority pathogen listed by the World Health Organization due to increasing levels of resistance to carbapenem classes of antibiotics. It causes wound and other nosocomial infections, which can be life-threatening. Hence, there is an urgent need for the development of new classes of antibiotics. Aim. To study the interaction of carabapenems with class D beta-lactamases (oxacillinases) and analyse drug resistance by studying enzyme–substrate complexes using modelling approaches as a means of establishing correlations with the phenotypic data. Methodology. The three-dimensional structures of carbapenems (doripenem, ertapenem, imipenem and meropenem) were obtained from DrugBank and screened against class D beta-lactamases. Further, the study was extended with their variants. The variants’ structure was homology-modelled using the Schrödinger Prime module (Schrödinger LLC, NY, USA). Results. The first discovered intrinsic beta-lactamase of Acinetobacter baumannii , OXA-51, had a binding energy value of −40.984 kcal mol−1, whereas other OXA-51 variants, such as OXA-64, OXA-110 and OXA-111, have values of −60.638, –66.756 and −67.751 kcal mol−1, respectively. The free energy values of OXA-51 variants produced better results than those of other groups. Conclusions. Imipenem and meropenem showed MIC values of 2 and 8 µg ml−1, respectively against OXA-51 in earlier studies, indicating that these are the most effective drugs for treatment of A. baumannii infection. According to our results, OXA-51 is an active enzyme that shows better interactions and is capable of hydrolyzing carbapenems. When correlating the hydrogen-bonding interaction with MIC values, the predicted results are in good agreement and might provide initial insights into performing similar studies related to OXA variants or other antibiotic–enzyme-based studies.

Catenulispora graminis sp. nov., a rhizobacterium from bamboo (Phyllostachys nigro var. henonis) rhizosphere soil

2012 ◽  
Vol 62 (Pt_11) ◽  
pp. 2589-2592 ◽  
Author(s):  
Hyo-Jin Lee ◽  
Song-Ih Han ◽  
Kyung-Sook Whang
Keyword(s):  
Type Species ◽  
Rhizosphere Soil ◽  
Major Fatty Acid ◽  
Rrna Gene ◽  
Phenotypic Data ◽  
Content Type ◽  
Dna Relatedness ◽  
Link Type ◽  
Isoprenoid Quinones ◽  
Type Strains

A novel actinobacterium, designated strain BR-34T, was isolated from rhizosphere soil of bamboo (Phyllostachys nigro var. henonis) sampled in Damyang, Korea. The strain was found to have morphological and chemotaxonomic characteristics typical of the genus Catenulispora . The strain contained iso-C16 : 0 as the major fatty acid and MK-9(H4), MK-9(H6) and MK-9(H8) as major isoprenoid quinones. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain BR-34T formed a cluster separate from members of the genus Catenulispora and was related most closely to Catenulispora acidiphila ID139908T (97.4 % similarity), Catenulispora rubra Aac-30T (97.3 %), Catenulispora yoronensis TT N02-20T (97.3 %) and Catenulispora subtropica TT 99-48T (97 %). However, the level of DNA–DNA relatedness between strain BR-34T and C. acidiphila ID139908T was only 45.32 %. Based on DNA–DNA relatedness, morphological and phenotypic data, strain BR-34T could be distinguished from the type strains of phylogenetically related species. It is therefore considered to represent a novel species of the genus Catenulispora , for which the name Catenulispora graminis sp. nov. is proposed. The type strain is BR-34T ( = KACC 15070T = NBRC 107755T).

scholarly journals Actinomadura geliboluensis sp. nov., isolated from soil

2012 ◽  
Vol 62 (Pt_8) ◽  
pp. 2011-2017 ◽  
Author(s):  
Anil Sazak ◽  
Mustafa Camas ◽  
Cathrin Spröer ◽  
Hans-Peter Klenk ◽  
Nevzat Sahin
Keyword(s):  
Cell Wall ◽  
Type Species ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Phenotypic Data ◽  
Content Type ◽  
Link Type ◽  
Acid Type ◽  
Gene Sequence Analysis ◽  
Taxonomic Approach

A novel actinobacterium, strain A8036T, isolated from soil, was investigated by using a polyphasic taxonomic approach. The organism formed extensively branched substrate hyphae that generated spiral chains of spores with irregular surfaces. The cell wall contained meso-diaminopimelic acid (type III) and cell-wall sugars were glucose, madurose, mannose and ribose. The predominant menaquinones were MK-9(H6) and MK-9(H4). The phospholipids were diphosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannosides. The major cellular fatty acids were iso-C16 : 0, C17 : 1 cis9, C16 : 0, C15 : 0 and 10-methyl C17 : 0. Based on 16S rRNA gene sequence analysis, the closest phylogenetic neighbours of strain A8036T were Actinomadura meyerae DSM 44715T (99.23 % similarity), Actinomadura bangladeshensis DSM 45347T (98.9 %) and Actinomadura chokoriensis DSM 45346T (98.3 %). However, DNA–DNA relatedness and phenotypic data demonstrated that strain A8036T could be clearly distinguished from the type strains of all closely related Actinomadura species. Strain A8036T is therefore considered to represent a novel species of the genus Actinomadura , for which the name Actinomadura geliboluensis sp. nov. is proposed. The type strain is A8036T ( = DSM 45508T = KCTC 19868T).

scholarly journals Microbacterium mangrovi sp. nov., an amylolytic actinobacterium isolated from mangrove forest soil

2014 ◽  
Vol 64 (Pt_10) ◽  
pp. 3513-3519 ◽  
Author(s):  
Learn-Han Lee ◽  
Adzzie-Shazleen Azman ◽  
Nurullhudda Zainal ◽  
Shu-Kee Eng ◽  
Nurul-Syakima Ab Mutalib ◽  
...  
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Peninsular Malaysia ◽  
Rrna Gene ◽  
Phenotypic Data ◽  
Dna Profile ◽  
Content Type ◽  
Link Type ◽  
Mangrove Soil ◽  
Agar Media

Strain MUSC 115T was isolated from mangrove soil of the Tanjung Lumpur river in the state of Pahang, Peninsular Malaysia. Cells of this strain stained Gram-positive and were non-spore-forming, short rods that formed yellowish-white colonies on different agar media. The taxonomy of strain MUSC 115T was studied by a polyphasic approach, and the organism showed a range of phylogenetic and chemotaxonomic properties consistent with those of the genus Microbacterium . The cell-wall peptidoglycan was of type B2β, containing the amino acids ornithine, alanine, glycine, glutamic acid and homoserine. The muramic acid was of the N-glycolyl form. The predominant menaquinones detected were MK-12, MK-13 and MK-11. The polar lipids consisted of phosphatidylglycerol, phosphoglycolipid, diphosphatidylglycerol, two unidentified lipids, three unidentified phospholipids and four unidentified glycolipids. The major fatty acids of the cell membrane were anteiso-C15 : 0 and anteiso-C17 : 0. The whole-cell sugars detected were ribose, glucose, mannose and galactose. Based on the 16S rRNA gene sequence, strain MUSC 115T showed the highest sequence similarity to Microbacterium immunditiarum SK 18T (98.1 %), M. ulmi XIL02T (97.8 %) and M. arborescens DSM 20754T (97.5 %) and lower sequence similarity to strains of other species of the genus Microbacterium . DNA–DNA hybridization experiments revealed a low level of DNA–DNA relatedness (less than 24 %) between strain MUSC 115T and the type strains of closely related species. Furthermore, BOX-PCR fingerprint comparison also indicated that strain MUSC 115T represented a unique DNA profile. The DNA G+C content determined was 70.9±0.7 mol%, which is lower than that of M. immunditiarum SK 18T. Based on the combination of genotypic and phenotypic data, it is proposed that strain MUSC 115T represents a novel species of the genus Microbacterium , for which the name Microbacterium mangrovi sp. nov. is proposed. The type strain is MUSC 115T ( = MCCC 1K00251T = DSM 28240T = NBRC 110089T).

Jeongeupia chitinilytica sp. nov., a chitinolytic bacterium isolated from soil

2013 ◽  
Vol 63 (Pt_3) ◽  
pp. 934-938 ◽  
Author(s):  
Wen-Ming Chen ◽  
Rey-Chang Chang ◽  
Chih-Yu Cheng ◽  
Yu-Wen Shiau ◽  
Shih-Yi Sheu
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Data ◽  
Polar Lipid Profile ◽  
Content Type ◽  
Link Type ◽  
Novel Bacterium

A novel bacterium, designated strain JchiT, was isolated from soil in Taiwan and characterized using a polyphasic approach. Cells of strain JchiT were aerobic, Gram-stain-negative, motile and rod-shaped. They contained poly-β-hydroxybutyrate granules and formed dark-yellow colonies. Growth occurred at 20–37 °C (optimum between 25 and 30 °C), at pH 6.0–8.0 (optimum between pH 7.0 and pH 8.0) and with 0–2 % NaCl (optimum between 0 and 1 %). Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain JchiT belonged to the genus Jeongeupia and that its closest neighbour was Jeongeupia naejangsanensis BIO-TAS4-2T (98.0 % sequence similarity). The major fatty acids (>10 %) of strain JchiT were summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and C18 : 1ω7c. The major cellular hydroxy fatty acid was C12 : 0 3-OH. The isoprenoid quinone was Q-8 and the genomic DNA G+C content was 66.1 mol%. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylserine and two unidentified phospholipids. The DNA–DNA relatedness value between strain JchiT and J. naejangsanensis BIO-TAS4-2T was about 41.0 %. On the basis of the genotypic and phenotypic data, strain JchiT represents a novel species in the genus Jeongeupia , for which the name Jeongeupia chitinilytica sp. nov. is proposed. The type strain is JchiT ( = BCRC 80367T  = KCTC 23701T).

scholarly journals Amycolatopsis rhabdoformis sp. nov., an actinomycete isolated from a tropical forest soil

2015 ◽  
Vol 65 (Pt_6) ◽  
pp. 1786-1793 ◽  
Author(s):  
Wallace Rafael Souza ◽  
Rafael Eduardo Silva ◽  
Michael Goodfellow ◽  
Kanungnid Busarakam ◽  
Fernanda Sales Figueiro ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
Gene Tree ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Phenotypic Data ◽  
Content Type ◽  
Link Type

Strain SB026T was isolated from Brazilian rainforest soil and its taxonomic position established using data from a polyphasic study. The organism showed a combination of chemotaxonomic and morphological features consistent with its classification in the genus Amycolatopsis and formed a branch in the Amycolatopsis 16S rRNA gene tree together with Amycolatopsis bullii NRRL B-24847T, Amycolatopsis plumensis NRRL B-24324T, Amycolatopsis tolypomycina DSM 44544T and Amycolatopsis vancoresmycina NRRL B-24208T. It was related most closely to A. bullii NRRL B-24847T (99.0 % 16S rRNA gene sequence similarity), but was distinguished from this strain by a low level of DNA–DNA relatedness (~46 %) and discriminatory phenotypic properties. Based on the combined genotypic and phenotypic data, it is proposed that the isolate should be classified in the genus Amycolatopsis as representing a novel species, Amycolatopsis rhabdoformis sp. nov. The type strain is SB026T ( = CBMAI 1694T = CMAA 1285T = NCIMB 14900T).

scholarly journals Elioraea rosea sp. nov., a plant promoting bacterium isolated from floodwater of a paddy field

2020 ◽  
Vol 70 (3) ◽  
pp. 2132-2136 ◽  
Author(s):  
Hyo-Jin Lee ◽  
Kyung-Sook Whang
Keyword(s):  
Paddy Field ◽  
Type Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Phenotypic Data ◽  
Content Type ◽  
Dna Relatedness ◽  
Link Type

A Gram-stain-negative bacterium, designated strain PF-30T, was isolated from floodwater of a paddy field in South Korea. Strain PF-30T was found to be a strictly aerobic, motile and pink-pigmented rods which can grow at 25–40 °C (optimum, 28 °C), at pH 5.0–9.0 (optimum pH 7.0) and at salinities of 0.5–3.0 % NaCl (optimum 0.5 % NaCl). Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain PF-30T belongs to the genus Elioraea , showing highest sequence similarity to Elioraea tepidiphila TU-7T (97.1%) and less than 91.3 % similarity with other members of the family Acetobacteraceae . The average nucleotide identity (ANI) and DNA–DNA relatedness between the strain PF-30T and E. tepidiphila TU-7T yielded an ANI value of 75.1 % and DNA–DNA relatedness of 11.7±0.7 %, respectively. The major fatty acids were identified as C18 : 0 and C18 : 1 ω7c. The predominant respiratory quinone was identified as Q-10. The DNA G+C content was determined to be 69.9 mol%. The strain PF-30T was observed to produce plant-growth-promoting materials such as indole-3-acetic acid (IAA), siderophore and phytase. On the basis of the results from phylogenetic, chemotaxonomic and phenotypic data, we concluded that strain PF-30T represents a novel species of the genus Elioraea , for which the name Elioraea rosea sp. nov. is proposed. The type strain is PF-30T (=KACC 19985T=NBRC 113984T).

Streptomyces ziwulingensis sp. nov., isolated from grassland soil

2013 ◽  
Vol 63 (Pt_4) ◽  
pp. 1545-1549 ◽  
Author(s):  
Yan Bing Lin ◽  
Xin Ye Wang ◽  
Ting Ting Wang ◽  
Shao Shan An ◽  
Peng Shi ◽  
...  
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
The Novel ◽  
Phenotypic Data ◽  
Grassland Soil ◽  
Content Type ◽  
Link Type ◽  
Hybridization Data ◽  
Antibacterial And Antifungal

A novel actinobacterium, designated strain F22T, was isolated from grassland soil collected from the Ziwuling area on the Loess Plateau, China. The novel strain was found to have morphological and chemotaxonomic characteristics typical of members of the genus Streptomyces . Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain F22T belonged to the genus Streptomyces , being most closely related to Streptomyces resistomycificus NBRC 12814T (98.28 % sequence similarity), Streptomyces ciscaucasicus NBRC 12872T (98.14 %), Streptomyces chartreusis NBRC 12753T (98.14 %) and Streptomyces canus NRRL B-1989T (98.14 %). In DNA–DNA hybridizations and comparisons of morphological and phenotypic data, strain F22T could be distinguished from all of its closest phylogenetic relatives. Strain F22T exhibited antibacterial and antifungal activity, especially against Staphylococcus aureus , Bacillus subtilis and Cylindrocarpon destructans. Based on the DNA–DNA hybridization data and morphological, phenotypic and phylogenetic evidence, strain F22T represents a novel species of the genus Streptomyces , for which the name Streptomyces ziwulingensis sp. nov. is proposed. The type strain is F22T ( = CCNWFX 0001T = JCM 18081T = ACCC41875T).

Croceimicrobium hydrocarbonivorans gen. nov., sp. nov., a novel marine bacterium isolated from a bacterial consortium that degrades polyethylene terephthalate

2021 ◽  
Vol 71 (4) ◽  
Author(s):  
Renju Liu ◽  
Qiliang Lai ◽  
Li Gu ◽  
Peisheng Yan ◽  
Zongze Shao
Keyword(s):  
Polyethylene Terephthalate ◽  
Type Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Phenotypic Data ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
The Family

A novel Gram-stain-negative, aerobic, gliding, rod-shaped and carotenoid-pigmented bacterium, designated A20-9T, was isolated from a microbial consortium of polyethylene terephthalate enriched from a deep-sea sediment sample from the Western Pacific. Growth was observed at salinities of 1–8 %, at pH 6.5–8 and at temperatures of 10–40 °C. The results of phylogenetic analyses based on the genome indicated that A20-9T formed a monophyletic branch affiliated to the family Schleiferiaceae , and the 16S rRNA gene sequences exhibited the maximum sequence similarity of 93.8 % with Owenweeksia hongkongensis DSM 17368T, followed by similarities of 90.4, 90.1 and 88.8 % with Phaeocystidibacter luteus MCCC 1F01079T, Vicingus serpentipes DSM 103558T and Salibacter halophilus MCCC 1K02288T, respectively. Its complete genome size was 4 035 598 bp, the genomic DNA G+C content was 43.2 mol%. Whole genome comparisons indicated that A20-9T and O. hongkongensis DSM 17368T shared 67.8 % average nucleotide identity, 62.7 % average amino acid identity value, 46.6% of conserved proteins and 17.8 % digital DNA–DNA hybridization identity. A20-9T contained MK-7 as the major respiratory quinone. Its major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phospatidylcholine; and the major fatty acids were iso-C15 : 0 (37.5 %), iso-C16 : 0 3-OH (12.4 %), and summed feature 3 (C16 : 1ω7c /C16 : 1ω6c, 11.6 %). Combining the genotypic and phenotypic data, A20-9T could be distinguished from the members of other genera within the family Schleiferiaceae and represents a novel genus, for which the name Croceimicrobium hydrocarbonivorans gen. nov., sp. nov. is proposed. The type strain is A20-9T (=MCCC 1A17358T =KCTC 72878T).

Nocardioides donggukensis sp. nov. and Hyunsoonleella aquatilis sp. nov., isolated from Jeongbang Waterfall on Jeju Island

2021 ◽  
Vol 71 (12) ◽  
Author(s):  
Inhyup Kim ◽  
Geeta Chhetri ◽  
Jiyoun Kim ◽  
Minchung Kang ◽  
Yoonseop So ◽  
...  
Keyword(s):  
Type Strain ◽  
Type Species ◽  
Bacterial Species ◽  
Jeju Island ◽  
Nucleotide Identity ◽  
Rrna Gene ◽  
Average Nucleotide Identity ◽  
Phenotypic Data ◽  
Content Type ◽  
Link Type

Two bacterial strains, designated MJB4T and SJ7T, were isolated from water samples collected from Jeongbang Falls on Jeju Island, Republic of Korea. Phylogenetic analysis of 16S rRNA gene sequences indicated that the two strains belonged to the genera Nocardioides and Hyunsoonleella , owing to their high similarities to Nocardioides jensenii DSM 29641T (97.5 %) and Hyunsoonleella rubra FA042 T (96.3 %), respectively. These values are much lower than the gold standard for bacterial species (98.7 %). The average nucleotide identity values between strains MJB4T, SJ7T and the reference strains, Nocardioides jensenii DSM 29641T, Nocardioides daejeonensis MJ31T and Hyunsoonleella flava T58T were 77.2, 75.9 and 75.4 %, respectively. Strains MJB4T and SJ7T and the type strains of the species involved in system incidence have average nucleotide identity and average amino acid threshold values of 60.1–82.6 % for the species boundary (95–96 %), which confirms that strains MJB4T and SJ7T represent two new species of genus Nocardioides and Hyunsoonleella , respectively. Based on phylogenetic and phenotypic data, strains MJB4T and SJ7T are considered to represent novel species of the genus Nocardioides and Hyunsoonleella , respectively, for which the names Nocardioides donggukensis sp. nov. (type strain MJB4T=KACC 21724T=NBRC 114402T) and Hyunsoonleella aquatilis sp. nov., (type strain SJ7T=KACC 21715T=NBRC 114486T) have been proposed.

Sulfurovum indicum sp. nov., a novel hydrogen- and sulfur-oxidizing chemolithoautotroph isolated from a deep-sea hydrothermal plume in the Northwestern Indian Ocean

2019 ◽  
Vol 71 (3) ◽  
Author(s):  
Shaobin Xie ◽  
Shasha Wang ◽  
Dengfeng Li ◽  
Zongze Shao ◽  
Qiliang Lai ◽  
...  
Keyword(s):  
Indian Ocean ◽  
Deep Sea ◽  
Type Species ◽  
Elemental Sulfur ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Phenotypic Data ◽  
Content Type ◽  
Link Type ◽  
Sulfur Oxidizing

A novel mesophilic, hydrogen-, and sulfur-oxidizing bacterium, designated strain ST-419T, was isolated from a deep-sea hydrothermal vent plume on the Carlsberg Ridge of the Northwestern Indian Ocean. The isolate was a Gram-staining-negative, non-motile and coccoid to oval-shaped bacterium. Growth was observed at 4–50 °C (optimum 37 °C), pH 5.0–8.6 (optimum pH 6.0) and 1.0–5.0 % (w/v) NaCl (optimum 3.0 %). ST-419T could grow chemlithoautotrophically with molecular hydrogen, sulfide, elemental sulfur and thiosulfate as energy sources. Molecular oxygen, nitrate and elemental sulfur could be used as electron acceptors. The predominant fatty acids were C16 : 1ω7c, C18 : 1ω7c and C16 : 0. The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. The respiratory quinone was menaquinone MK-6 and the G+C content of the genomic DNA was 42.4 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that ST-419T represented a member of genus Sulfurovum and was most closely related to Sulfurovum riftiae 1812ET, with 97.6 % sequence similarity. The average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between ST-419T and S. riftiae 1812ET were 74.6 and 19.6 %, respectively. The combined genotypic and phenotypic data indicate that ST-419T represents a novel species within the genus Sulfurovum , for which the name Sulfurovum indicum sp. nov. is proposed. The type strain is ST-419T (=MCCC 1A17954T=KCTC 25164T).

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