A novel structurally characterized haloacid dehalogenase superfamily phosphatase from Thermococcus thioreducens with diverse substrate specificity

2019 ◽  
Vol 75 (8) ◽  
pp. 743-752
Author(s):  
Petra Havlickova ◽  
Vitezslav Brinsa ◽  
Jiri Brynda ◽  
Petr Pachl ◽  
Tatyana Prudnikova ◽  
...  
Keyword(s):  
Sequence Similarity ◽  
Thermophilic Enzyme ◽  
Haloacid Dehalogenase ◽  
Computational Docking ◽  
Cell Parameters ◽  
X Ray Crystallography ◽  
The Family ◽  
Had Superfamily ◽  
Characteristic Features ◽  
Hydrolysis Of

The haloacid dehalogenase (HAD) superfamily is one of the largest known groups of enzymes and the majority of its members catalyze the hydrolysis of phosphoric acid monoesters into a phosphate ion and an alcohol. Despite the fact that sequence similarity between HAD phosphatases is generally very low, the members of the family possess some characteristic features, such as a Rossmann-like fold, HAD signature motifs or the requirement for Mg2+ ion as an obligatory cofactor. This study focuses on a new hypothetical HAD phosphatase from Thermococcus thioreducens. The protein crystallized in space group P21212, with unit-cell parameters a = 66.3, b = 117.0, c = 33.8 Å, and the crystals contained one molecule in the asymmetric unit. The protein structure was determined by X-ray crystallography and was refined to 1.75 Å resolution. The structure revealed a putative active site common to all HAD members. Computational docking into the crystal structure was used to propose substrates of the enzyme. The activity of this thermophilic enzyme towards several of the selected substrates was confirmed at temperatures of 37°C as well as 60°C.

scholarly journals Genome-wide analysis of haloacid dehalogenase genes reveals their function in phosphate starvation responses in rice

PLoS ONE ◽  
2021 ◽  
Vol 16 (1) ◽  
pp. e0245600
Author(s):  
Zezhen Du ◽  
Suren Deng ◽  
Zixuan Wu ◽  
Chuang Wang
Keyword(s):  
Bioinformatics Analysis ◽  
Sequence Similarity ◽  
Motif Analysis ◽  
Systematic Classification ◽  
Diverse Range ◽  
Haloacid Dehalogenase ◽  
Genome Wide ◽  
Pi Starvation ◽  
Had Superfamily ◽  
Pi Stress

The HAD superfamily is named after the halogenated acid dehalogenase found in bacteria, which hydrolyses a diverse range of organic phosphate substrates. Although certain studies have shown the involvement of HAD genes in Pi starvation responses, systematic classification and bioinformatics analysis of the HAD superfamily in plants is lacking. In this study, 41 and 40 HAD genes were identified by genomic searching in rice and Arabidopsis, respectively. According to sequence similarity, these proteins are divided into three major groups and seven subgroups. Conserved motif analysis indicates that the majority of the identified HAD proteins contain phosphatase domains. A further structural analysis showed that HAD proteins have four conserved motifs and specified cap domains. Fewer HAD genes show collinearity relationships in both rice and Arabidopsis, which is consistent with the large variations in the HAD genes. Among the 41 HAD genes of rice, the promoters of 28 genes contain Pi-responsive cis-elements. Mining of transcriptome data and qRT-PCR results showed that at least the expression of 17 HAD genes was induced by Pi starvation in shoots or roots. These HAD proteins are predicted to be involved in intracellular or extracellular Po recycling under Pi stress conditions in plants.

Succinatimonas hippei gen. nov., sp. nov., isolated from human faeces

2010 ◽  
Vol 60 (8) ◽  
pp. 1788-1793 ◽  
Author(s):  
Masami Morotomi ◽  
Fumiko Nagai ◽  
Yohei Watanabe ◽  
Ryuichiro Tanaka
Keyword(s):  
Sequence Similarity ◽  
Major Fatty Acid ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
Phenotypic Characteristics ◽  
Human Faeces ◽  
Gene Sequence Analysis ◽  
The Family ◽  
Hydrolysis Of ◽  
Indole Production

A novel strictly anaerobic, non-spore-forming, non-motile, non-flagellated, rod-shaped, Gram-negative bacterium (YIT 12066T) was isolated from human faeces. The isolate was negative for catalase, oxidase, urease, hydrolysis of aesculin and gelatin, nitrate reduction and indole production. The major end products of glucose metabolism were succinate and acetate. The major cellular fatty acids (>10 %) were C14 : 0, C18 : 1 ω7c, C18 : 1 ω9c, C16 : 1 ω7c and C16 : 0. The G+C content of the DNA was 40.3 mol%. 16S rRNA gene sequence analysis showed that strain YIT 12066T was most closely related to members of the family Succinivibrionaceae, with sequence similarity of 92–87 %. However, some phenotypic characteristics such as cellular morphology and the major fatty acid profile of strain YIT 12066T were markedly different from those of other members of the family Succinivibrionaceae. On the basis of both phylogenetic and phenotypic evidence, it is suggested that strain YIT 12066T represents a novel species in a new genus, for which the name Succinatimonas hippei gen. nov., sp. nov. is proposed; the type strain of Succinatimonas hippei is YIT 12066T (=DSM 22608T =JCM 16073T).

scholarly journals A preliminary X-ray study of 3-deoxy-D-manno-oct-2-ulosonic acid 8-phosphate phosphatase (YrbI) fromBurkholderia pseudomallei

2015 ◽  
Vol 71 (6) ◽  
pp. 790-793 ◽  
Author(s):  
Jimin Park ◽  
Daeun Lee ◽  
Mi-Sun Kim ◽  
Dae Yong Kim ◽  
Dong Hae Shin
Keyword(s):  
Burkholderia Pseudomallei ◽  
Large Family ◽  
Orthorhombic Space Group ◽  
Haloacid Dehalogenase ◽  
X Ray ◽  
Cell Parameters ◽  
Had Superfamily ◽  
Function Relationship ◽  
Relationship Of ◽  
Ulosonic Acid

3-Deoxy-D-manno-oct-2-ulosonic acid 8-phosphate phosphatase (YrbI), the third enzyme in the pathway for the biosynthesis of 3-deoxy-D-manno-oct-2-ulosonic acid (KDO), hydrolyzes KDO 8-phosphate to KDO and inorganic phosphate. YrbI belongs to the haloacid dehalogenase (HAD) superfamily, which is a large family of magnesium-dependent phosphatase/phosphotransferase enzymes. In this study, YrbI fromBurkholderia pseudomallei, the causative agent of melioidosis, has been cloned, expressed, purified and crystallized. Synchrotron X-ray data were also collected to 2.25 Å resolution. The crystal belonged to the primitive orthorhombic space groupP212121, with unit-cell parametersa= 63.7,b= 97.5,c= 98.0 Å. A full structural determination is in progress to elucidate the structure–function relationship of this protein.

Monoglobus pectinilyticus gen. nov., sp. nov., a pectinolytic bacterium isolated from human faeces.

2020 ◽  
Author(s):  
CC Kim ◽  
WJ Kelly ◽  
ML Patchett ◽  
GW Tannock ◽  
Z Jordens ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Middle Lamella ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Citrus Peel ◽  
Human Faeces ◽  
The Family

© 2017 IUMS. A novel anaerobic pectinolytic bacterium (strain 14T) was isolated from human faeces. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 14T belonged to the family Ruminococcaceae, but was located separately from known clostridial clusters within the taxon. The closest cultured relative of strain 14T was Acetivibrio cellulolyticus (89.7% sequence similarity). Strain 14T shared ~99% sequence similarity with cloned 16S rRNA gene sequences from uncultured bacteria derived from the human gut. Cells were Gram-stain-positive, non-motile cocci approximately 0.6μm in diameter. Strain 14T fermented pectins from citrus peel, apple, and kiwifruit as well as carbohydrates that are constituents of pectins and hemicellulose, such as galacturonic acid, xylose, and arabinose. TEM images of strain 14T, cultured in association with plant tissues, suggested extracellular fibrolytic activity associated with the bacterial cells, forming zones of degradation in the pectin-rich regions of middle lamella. Phylogenetic and phenotypic analysis supported the differentiation of strain 14T as a novel genus in the family Ruminococcaceae. The name Monoglobus pectinilyticus gen. nov., sp. nov. is proposed; the type strain is 14T (JCM 31914T=DSM 104782T).

scholarly journals Transcriptomic and Proteomic Analyses Reveal the Diversity of Venom Components from the Vaejovid Scorpion Serradigitus gertschi

Toxins ◽  
2018 ◽  
Vol 10 (9) ◽  
pp. 359 ◽  
Author(s):  
Maria Romero-Gutiérrez ◽  
Carlos Santibáñez-López ◽  
Juana Jiménez-Vargas ◽  
Cesar Batista ◽  
Ernesto Ortiz ◽  
...  
Keyword(s):  
Serine Proteases ◽  
De Novo ◽  
Sequence Similarity ◽  
Scorpion Venom ◽  
Secretory Proteins ◽  
Host Defense Peptides ◽  
The Family ◽  
Pathogenesis Related ◽  
Molecular Masses

To understand the diversity of scorpion venom, RNA from venomous glands from a sawfinger scorpion, Serradigitus gertschi, of the family Vaejovidae, was extracted and used for transcriptomic analysis. A total of 84,835 transcripts were assembled after Illumina sequencing. From those, 119 transcripts were annotated and found to putatively code for peptides or proteins that share sequence similarities with the previously reported venom components of other species. In accordance with sequence similarity, the transcripts were classified as potentially coding for 37 ion channel toxins; 17 host defense peptides; 28 enzymes, including phospholipases, hyaluronidases, metalloproteases, and serine proteases; nine protease inhibitor-like peptides; 10 peptides of the cysteine-rich secretory proteins, antigen 5, and pathogenesis-related 1 protein superfamily; seven La1-like peptides; and 11 sequences classified as “other venom components”. A mass fingerprint performed by mass spectrometry identified 204 components with molecular masses varying from 444.26 Da to 12,432.80 Da, plus several higher molecular weight proteins whose precise masses were not determined. The LC-MS/MS analysis of a tryptic digestion of the soluble venom resulted in the de novo determination of 16,840 peptide sequences, 24 of which matched sequences predicted from the translated transcriptome. The database presented here increases our general knowledge of the biodiversity of venom components from neglected non-buthid scorpions.

Preparation and structural analysis of (±)-threo-ritalinic acid

2013 ◽  
Vol 69 (11) ◽  
pp. 1225-1228 ◽  
Author(s):  
Sara Wyss ◽  
Irmgard A. Werner ◽  
W. Bernd Schweizer ◽  
Simon M. Ametamey ◽  
Selena Milicevic Sephton
Keyword(s):  
Methyl Ester ◽  
Free Acid ◽  
Nmr Analysis ◽  
Intermolecular Hydrogen Bonds ◽  
X Ray ◽  
X Ray Crystallography ◽  
Ph Values ◽  
Ritalinic Acid ◽  
Methyl Phenidate ◽  
Hydrolysis Of

Hydrolysis of the methyl ester (±)-threo-methyl phenidate afforded the free acid in 40% yield,viz.(±)-threo-ritalinic acid, C13H17NO2. Hydrolysis and subsequent crystallization were accomplished at pH values between 5 and 7 to yield colourless prisms which were analysed by X-ray crystallography. Crystals of (±)-threo-ritalinic acid belong to theP21/nspace group and form intermolecular hydrogen bonds. An antiperiplanar disposition of the H atoms of the (HOOC—)CH—CHpygroup (py is pyridine) was found in both the solid (diffraction analysis) and solution state (NMR analysis). It was also determined that (±)-threo-ritalinic acid conforms to the minimization of negativegauche+–gauche−interactions.

Chemistry of oxylipin pathways in marine diatoms

2007 ◽  
Vol 79 (4) ◽  
pp. 481-490 ◽  
Author(s):  
Angelo Fontana ◽  
Giuliana d'Ippolito ◽  
Adele Cutignano ◽  
Antonio Miralto ◽  
Adrianna Ianora ◽  
...  
Keyword(s):  
Higher Plants ◽  
Larval Growth ◽  
Marine Macroalgae ◽  
High Concentration ◽  
Marine Diatoms ◽  
Fatty Acid Derivatives ◽  
The Family ◽  
Hydrolysis Of ◽  
Catalyzed Oxidation

Oxylipins are important signal transduction molecules widely distributed in animals and plants where they regulate a variety of events associated with physiological and pathological processes. The family embraces several different metabolites that share a common origin from the oxygenase-catalyzed oxidation of polyunsaturated fatty acids. The biological role of these compounds has been especially studied in mammalians and higher plants, although a varied and very high concentration of these products has also been reported from marine macroalgae. This article gives a summary of our results concerning the oxylipin chemistry of marine diatoms, a major class of planktonic microalgae that discourage predation from their natural grazers, zooplanktonic copepods, using chemical warfare. These apparently harmless microscopic cells produce a plethora of oxylipins, including short-chain unsaturated aldehydes, hydroxyl-, keto-, and epoxyhydroxy fatty acid derivatives, that induce reproductive failure in copepods through abortions, congenital malformations, and reduced larval growth. The biochemical process involved in the production of these compounds shows a simple regulation based on decompartmentation and mixing of preexisting enzymes and requires hydrolysis of chloroplast-derived glycolipids to feed the downstream activities of C16 and C20 lipoxygenases.

Aggregatimonas Sangjinii Gen. Nov., Sp. Nov., A Novel Silver Nanoparticle Synthesizing Bacterium Belonging to the Family Flavobacteriaceaee

2021 ◽  
Author(s):  
Dawoon Chung ◽  
Jaoon Young Hwan Kim ◽  
Kyung Woo Kim ◽  
Yong Min Kwon
Keyword(s):  
16S Rrna ◽  
Genome Sequence ◽  
Sequence Similarity ◽  
Whole Genome Sequence ◽  
Rrna Gene ◽  
Aerobic Bacterium ◽  
16S Rrna Sequence ◽  
Respiratory Quinone ◽  
The Family ◽  
The Media

Abstract A gram-negative, orange-pigmented, non-flagellated, gliding, rod-shaped, and aerobic bacterium, designated strain F202Z8T, was isolated from a rusty iron plate found in the intertidal region of Taean, South Korea. Notably, this strain synthesized silver nanoparticles (AgNPs), and 17 putative genes responsible for the synthesis of AgNPs were found in its genome. The complete genome sequence of strain F202Z8T is 4,723,614 bp, with 43.26% G + C content. Phylogenetic analysis based on 16S rRNA gene sequence revealed that strain F202Z8T forms a distinct lineage with closely related genera Maribacter, Pelagihabitans, Pseudozobellia, Zobellia, Pricia, and Costertonia belonging to the family Flavobacteriaceae. The 16S rRNA sequence similarity was < 94.5%. The digital DNA–DNA hybridization and average nucleotide identity values calculated from the whole genome-sequence comparison between strain F202Z8T and other members of the family Flavobacteriaceae were in the ranges of 12.7–16.9% and 70.3–74.4%, respectively. Growth was observed at 15–33°C (optimally at 30°C), at pH 6.5–7.5 (optimally at pH 7.0), and with the addition of 2.5–4.5% (w/v) NaCl to the media (optimally at 4.0%). The predominant cellular fatty acids were iso-C15: 0, iso-C15 :1 G, and iso-C17 :0 3-OH; the major respiratory quinone was MK-6. Polar lipids included phosphatidylethanolamine, five unidentified lipids, and two unidentified aminolipids. Our polyphasic taxonomic results suggested that this strain represents a novel species of a novel genus in the family Flavobacteriaceae, for which the name Aggregatimonas sangjinii gen. nov., sp. nov. is proposed. The type strain of Aggregatimonas sangjinii is F202Z8T (= KCCM 43411T = LMG 31494T).

An intergenic G-rich region in Leishmania tarentolae kinetoplast maxicircle DNA is a pan-edited cryptogene encoding ribosomal protein S12

1992 ◽  
Vol 12 (1) ◽  
pp. 56-67
Author(s):  
D A Maslov ◽  
N R Sturm ◽  
B M Niner ◽  
E S Gruszynski ◽  
M Peris ◽  
...  
Keyword(s):  
Amino Acid ◽  
Ribosomal Protein ◽  
Ribosomal Proteins ◽  
Sequence Similarity ◽  
Rich Region ◽  
Leishmania Tarentolae ◽  
Significant Sequence Similarity ◽  
The Family ◽  
Intergenic Regions ◽  
Ribosomal Protein S12

Six short G-rich intergenic regions in the maxicircle of Leishmania tarentolae are conserved in location and polarity in two other kinetoplastid species. We show here that G-rich region 6 (G6) represents a pan-edited cryptogene which contains at least two domains edited independently in a 3'-to-5' manner connected by short unedited regions. In the completely edited RNA, 117 uridines are added at 49 sites and 32 uridines are deleted at 13 sites, creating a translated 85-amino-acid polypeptide. Similar polypeptides are probably encoded by pan-edited G6 transcripts in two other species. The G6 polypeptide has significant sequence similarity to the family of S12 ribosomal proteins. A minicircle-encoded gRNA overlaps 12 editing sites in G6 mRNA, and chimeric gRNA/mRNA molecules were shown to exist, in agreement with the transesterification model for editing.

Muriicola soli sp. nov., isolated from soil

2021 ◽  
Vol 71 (7) ◽  
Author(s):  
Hye Jeong Kang ◽  
Min-Kyeong Kim ◽  
Su Gwon Roh ◽  
Seung Bum Kim
Keyword(s):  
Related Species ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
Optimum Ph ◽  
Genomic Characterization

A Gram-stain-negative, oxidase-positive, catalase-positive, aerobic, orange-pigmented, rod-shaped and non-motile bacterium designated strain MMS17-SY002T was isolated from island soil. The isolate grew at 20–37 °C (optimum, 30 °C), at pH 6.0–9.5 (optimum, pH 7) and in the presence of 0.5–4.0 % (w/v) NaCl (optimum, 2.0 %). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain MMS17-SY002T was mostly related to the genus Muriicola of the family Flavobacteriaceae and had highest sequence similarity of 96.82 % to Muriicola marianensis A6B8T and Muriicola jejuensis EM44T, but formed a distinct phylogenetic line within the genus. Chemotaxonomic analyses showed that menaquinone 6 was the predominant isoprenoid quinone, the major fatty acids were iso-C15 : 1 G and iso-C15 : 0, and the diagnostic polar lipid was phosphatidylethanolamine. The genomic DNA G+C content was 42.4 mol%. Strain MMS17-SY002T could be distinguished from related species by the combination of trypsin, α-chymotrypsin, acid phosphatase, naphthol-AS-BI-phosphohydrolase, α-galactosidase, β-galactosidase and β-glucosidase activities. The orthologous average nucleotide identity between the genomes of strain MMS17-SY002T and M. jejuensis and that between the strain and M. marianensis A6B8T were 73.26 and 73.33%, respectively, thus confirming the separation of the strain from related species at species level. Based on the phenotypic, phylogenetic, chemotaxonomic and genomic characterization, MMS17-SY002T should be recognized as a novel species of the genus Muriicola , for which the name Muriicola soli sp. nov. is proposed. The type strain is MMS17-SY002T (=KCTC 62790T=JCM 32370T).

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