scholarly journals AatA Is a Novel Autotransporter and Virulence Factor of Avian Pathogenic Escherichia coli

2009 ◽  
Vol 78 (3) ◽  
pp. 898-906 ◽  
Author(s):  
Ganwu Li ◽  
Yaping Feng ◽  
Subhashinie Kariyawasam ◽  
Kelly A. Tivendale ◽  
Yvonne Wannemuehler ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Amino Acid ◽  
Chicken Embryo Fibroblast ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Virulence Plasmid ◽  
Passenger Domain ◽  
Reading Frame ◽  
E Coli ◽  
Amino Acid Signal Peptide

ABSTRACT Autotransporters (AT) are widespread in Gram-negative bacteria, and many of them are involved in virulence. An open reading frame (APECO1_O1CoBM96) encoding a novel AT was located in the pathogenicity island of avian pathogenic Escherichia coli (APEC) O1's virulence plasmid, pAPEC-O1-ColBM. This 3.5-kb APEC autotransporter gene (aatA) is predicted to encode a 123.7-kDa protein with a 25-amino-acid signal peptide, an 857-amino-acid passenger domain, and a 284-amino-acid β domain. The three-dimensional structure of AatA was also predicted by the threading method using the I-TASSER online server and then was refined using four-body contact potentials. Molecular analysis of AatA revealed that it is translocated to the cell surface, where it elicits antibody production in infected chickens. Gene prevalence analysis indicated that aatA is strongly associated with E. coli from avian sources but not with E. coli isolated from human hosts. Also, AatA was shown to enhance adhesion of APEC to chicken embryo fibroblast cells and to contribute to APEC virulence.

scholarly journals Adhesion, Invasion, and Agglutination Mediated by Two Trimeric Autotransporters in the Human Uropathogen Proteus mirabilis

2010 ◽  
Vol 78 (11) ◽  
pp. 4882-4894 ◽  
Author(s):  
Praveen Alamuri ◽  
Martin Löwer ◽  
Jan A. Hiss ◽  
Stephanie D. Himpsl ◽  
Gisbert Schneider ◽  
...  
Keyword(s):  
Proteus Mirabilis ◽  
Three Dimensional ◽  
Beta Sheets ◽  
Surface Proteins ◽  
Matrix Proteins ◽  
Dimensional Structure ◽  
Passenger Domain ◽  
Cell Monolayers ◽  
E Coli ◽  
Surface Adhesins

ABSTRACT Fimbriae of the human uropathogen Proteus mirabilis are the only characterized surface proteins that contribute to its virulence by mediating adhesion and invasion of the uroepithelia. PMI2122 (AipA) and PMI2575 (TaaP) are annotated in the genome of strain HI4320 as trimeric autotransporters with “adhesin-like” and “agglutinating adhesin-like” properties, respectively. The C-terminal 62 amino acids (aa) in AipA and 76 aa in TaaP are homologous to the translocator domains of YadA from Yersinia enterocolitica and Hia from Haemophilus influenzae. Comparative protein modeling using the Hia three-dimensional structure as a template predicted that each of these domains would contain four antiparallel beta sheets and that they formed homotrimers. Recombinant AipA and TaaP were seen as ∼28 kDa and ∼78 kDa, respectively, in Escherichia coli, and each also formed high-molecular-weight homotrimers, thus supporting this model. E. coli synthesizing AipA or TaaP bound to extracellular matrix proteins with a 10- to 60-fold-higher level of affinity than the control strain. Inactivation of aipA in P. mirabilis strains significantly (P < 0.01) reduced the mutants' ability to adhere to or invade HEK293 cell monolayers, and the functions were restored upon complementation. A 51-aa-long invasin region in the AipA passenger domain was required for this function. E. coli expressing TaaP mediated autoagglutination, and a taaP mutant of P. mirabilis showed significantly (P < 0.05) more reduced aggregation than HI4320. Gly-247 in AipA and Gly-708 in TaaP were indispensable for trimerization and activity. AipA and TaaP individually offered advantages to P. mirabilis in a murine model. This is the first report characterizing trimeric autotransporters in P. mirabilis as afimbrial surface adhesins and autoagglutinins.

scholarly journals RNA minihelices as model substrates for ATP/CTP:tRNA nucleotidyltransferase

1997 ◽  
Vol 327 (3) ◽  
pp. 847-851 ◽  
Author(s):  
Zengji LI ◽  
Yue SUN ◽  
L. David THURLOW
Keyword(s):  
Escherichia Coli ◽  
Saccharomyces Cerevisiae ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Single Base ◽  
Three Dimensional Structure ◽  
E Coli ◽  
Base Identity

Twenty-one RNA minihelices, resembling the coaxially stacked acceptor- /T-stems and T-loop found along the top of a tRNA's three-dimensional structure, were synthesized and used as substrates for ATP/CTP:tRNA nucleotidyltransferases from Escherichia coli and Saccharomyces cerevisiae. The sequence of nucleotides in the loop varied at positions corresponding to residues 56, 57 and 58 in the T-loop of a tRNA. All minihelices were substrates for both enzymes, and the identity of bases in the loop affected the interaction. In general, RNAs with purines in the loop were better substrates than those with pyrimidines, although no single base identity absolutely determined the effectiveness of the RNA as substrate. RNAs lacking bases near the 5ʹ-end were good substrates for the E. coli enzyme, but were poor substrates for that from yeast. The apparent Km values for selected minihelices were 2-3 times that for natural tRNA, and values for apparent Vmax were lowered 5-10-fold.

scholarly journals Identification of a positive regulator of the cell cycle ubiquitin-conjugating enzyme Cdc34 (Ubc3).

1996 ◽  
Vol 16 (2) ◽  
pp. 677-684 ◽  
Author(s):  
J A Prendergast ◽  
C Ptak ◽  
D Kornitzer ◽  
C N Steussy ◽  
R Hodgins ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Amino Acid ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Temperature Sensitive ◽  
Reading Frame ◽  
Positive Regulator ◽  
Morphological Defects ◽  
Ubiquitin Conjugating Enzyme ◽  
Conjugating Enzyme

The Cdc34 (Ubc3) ubiquitin-conjugating enzyme from Saccharomyces cerevisiae plays an essential role in the progression of cells from the G1 to S phase of the cell division cycle. Using a high-copy suppression strategy, we have identified a yeast gene (UBS1) whose elevated expression suppresses the conditional cell cycle defects associated with cdc34 mutations. The UBS1 gene encodes a 32.2-kDa protein of previously unknown function and is identical in sequence to a genomic open reading frame on chromosome II (GenBank accession number Z36034). Several lines of evidence described here indicate that Ubs1 functions as a general positive regulator of Cdc34 activity. First, overexpression of UBS1 suppresses not only the cell proliferation and morphological defects associated with cdc34 mutants but also the inability of cdc34 mutant cells to degrade the general amino acid biosynthesis transcriptional regulator, Gcn4. Second, deletion of the UBS1 gene profoundly accentuates the cell cycle defect when placed in combination with a cdc34 temperature-sensitive allele. Finally, a comparison of the Ubs1 and Cdc34 polypeptide sequences reveals two noncontiguous regions of similarity, which, when projected onto the three-dimensional structure of a ubiquitin-conjugating enzyme, define a single region situated on its surface. While cdc34 mutations corresponding to substitutions outside this region are suppressed by UBS1 overexpression, Ubs1 fails to suppress amino acid substitutions made within this region. Taken together with other findings, the allele specificity exhibited by UBS1 expression suggests that Ubs1 regulates Cdc34 by interaction or modification.

scholarly journals Characteristics of a New Enantioselective Thermostable Dipeptidase from Brevibacillus borstelensis BCS-1 and Its Application to Synthesis of a d-Amino-Acid-Containing Dipeptide

2004 ◽  
Vol 70 (3) ◽  
pp. 1570-1575 ◽  
Author(s):  
Dae Heoun Baek ◽  
Jae Jun Song ◽  
Seok-Joon Kwon ◽  
Chung Park ◽  
Chang-Min Jung ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Amino Acid ◽  
Nucleotide Sequence ◽  
Amino Acid Sequence ◽  
Open Reading Frame ◽  
Nucleotide Sequence Analysis ◽  
Reading Frame ◽  
E Coli ◽  
Specificity Constant ◽  
Optimal Ph

ABSTRACT A new thermostable dipeptidase gene was cloned from the thermophile Brevibacillus borstelensis BCS-1 by genetic complementation of the d-Glu auxotroph Escherichia coli WM335 on a plate containing d-Ala-d-Glu. Nucleotide sequence analysis revealed that the gene included an open reading frame coding for a 307-amino-acid sequence with an M r of 35,000. The deduced amino acid sequence of the dipeptidase exhibited 52% similarity with the dipeptidase from Listeria monocytogenes. The enzyme was purified to homogeneity from recombinant E. coli WM335 harboring the dipeptidase gene from B. borstelensis BCS-1. Investigation of the enantioselectivity (E) to the P1 and P1′ site of Ala-Ala revealed that the ratio of the specificity constant (k cat /Km ) for l-enantioselectivity to the P1 site of Ala-Ala was 23.4 � 2.2 [E = (k cat /Km ) l,d /(k cat /Km ) d,d ], while the d-enantioselectivity to the P1′ site of Ala-Ala was 16.4 � 0.5 [E = (k cat /Km ) l,d /(k cat /Km ) l,l ] at 55�C. The enzyme was stable up to 55�C, and the optimal pH and temperature were 8.5 and 65�C, respectively. The enzyme was able to hydrolyze l-Asp-d-Ala, l-Asp-d-AlaOMe, Z-d-Ala-d-AlaOBzl, and Z-l-Asp-d-AlaOBzl, yet it could not hydrolyze d-Ala-l-Asp, d-Ala-l-Ala, d-AlaNH2, and l-AlaNH2. The enzyme also exhibited β-lactamase activity similar to that of a human renal dipeptidase. The dipeptidase successfully synthesized the precursor of the dipeptide sweetener Z-l-Asp-d-AlaOBzl.

Comparison of the Amino Acid Sequence of L–Mandelate Dehydrogenase From Rhodotorula Graminis With Other L–2–Hydroxyacid Dehydrogenase Enzyme and its Primary Structure Prediction

2012 ◽  
Author(s):  
Rosli Md. Illias ◽  
Graeme A. Reid ◽  
Nadzarah A. Wahab
Keyword(s):  
Escherichia Coli ◽  
Amino Acid ◽  
Lactate Dehydrogenase ◽  
Primary Structure ◽  
Structure Prediction ◽  
Three Dimensional ◽  
Glycolate Oxidase ◽  
Dimensional Structure ◽  
Flavocytochrome B2 ◽  
Hansenula Anomala

Perbandingan struktur primer L(+)–mendalate dehydrogenase (L–MDH) daripada yis Rhodotorula graminis dengan protein lain di dalam bank data protein menunjukkan persamaan di antara protein ini dengan kumpulan enzim L–2–hidroksiasid dehidrogenase. LMDH daripada R. graminis mempamerkan kesamaan antara 26–42% kepada L–lactate dehidrogenase daripada Sacchomoryces cerevisiae, L–lactate dehidrogenase daripada Hansenula anomala, glikolat oksida daripada bayam, L–laktat dehidrogenase daripada Escherichia coli, LMDH daripada Psedomonas putida dan laktat–2 monooksigenase daripada Mycobakterium smegmatis. Asid amino yang penting secara strukturnya bagi LMDH diramalkan secara perbandingan dengan bahagian penting domain sitokram dan domain perlekatan FMN yang diperoleh daripada struktur tiga dimensi L–laktat dehidrogenase daripada Sacchoromyces cerevisiae. Kata kunci: L-MDH; Rhodotorula gramisis; L(+)-mandalate dehydrogenase; asid amino,flavocytochrome b2 A comparison of the primary structure or L–mandelate dehydrogenase (L–MDH) from Rhodotorula graminis with other proteins from the protein databank suggests that there is similarity between this protein and L–2–hydroxyacid dehydrogenase enzymes. R graminis LMDH exhibits 26–42% identity to L–lactate dehydrogenase from Saccharomyces cerevisiae, L–lactate dehydrogenase from Hansenula anomala, glycolate oxidase from spinach, L–lactate dehydrogenase from Escherichia coli, L–mandelate dehydrogenase from Pseudomonas putida and lactate–2–monooxygenase from Mycobacterium smegmatis. Structurally conserved amino acids are predicted from LMDH sequences corresponding to important regions of the cytochrome and FMN–binding domain defined from the known three–dimensional structure of the L–lactate dehyrogenase from Sacchoromyces cerevisiae. Key words: L-MDH; Rhodotorula graminis; L-mandelate dehydrogenase; amino acid;flavocytochrome b2

scholarly journals A Tetrahydrofolate-Dependent O-Demethylase, LigM, Is Crucial for Catabolism of Vanillate and Syringate in Sphingomonas paucimobilis SYK-6

2005 ◽  
Vol 187 (6) ◽  
pp. 2030-2037 ◽  
Author(s):  
Tomokuni Abe ◽  
Eiji Masai ◽  
Keisuke Miyauchi ◽  
Yoshihiro Katayama ◽  
Masao Fukuda
Keyword(s):  
Escherichia Coli ◽  
Amino Acid ◽  
Nucleotide Sequence ◽  
Double Mutant ◽  
Open Reading Frame ◽  
Sphingomonas Paucimobilis ◽  
Reading Frame ◽  
E Coli ◽  
Demethylase Activity ◽  
Specific Activities

ABSTRACT Vanillate and syringate are converted into protocatechuate (PCA) and 3-O-methylgallate (3MGA), respectively, by O-demethylases in Sphingomonas paucimobilis SYK-6. PCA is further degraded via the PCA 4,5-cleavage pathway, while 3MGA is degraded through multiple pathways in which PCA 4,5-dioxygenase (LigAB), 3MGA 3,4-dioxygenase (DesZ), and an unidentified 3MGA O-demethylase and gallate dioxygenase are participants. For this study, we isolated a 4.7-kb SmaI fragment that conferred on Escherichia coli the activity required for the conversion of vanillate to PCA. The nucleotide sequence of this fragment revealed an open reading frame of 1,413 bp (ligM), the deduced amino acid sequence of which showed 49% identity with that of the tetrahydrofolate (H4folate)-dependent syringate O-demethylase gene (desA). The metF and ligH genes, which are thought to be involved in H4folate-mediated C1 metabolism, were located just downstream of ligM. The crude LigM enzyme expressed in E. coli converted vanillate and 3MGA to PCA and gallate, respectively, with similar specific activities, and only in the presence of H4folate; however, syringate was not a substrate for LigM. The disruption of ligM led to significant growth retardation on both vanillate and syringate, indicating that ligM is involved in the catabolism of these substrates. The ability of the ligM mutant to transform vanillate was markedly decreased, and this mutant completely lost the 3MGA O-demethylase activity. A ligM desA double mutant completely lost the ability to transform vanillate, thus indicating that desA also contributes to vanillate degradation. All of these results indicate that ligM encodes vanillate/3MGA O-demethylase and plays an important role in the O demethylation of vanillate and 3MGA, respectively.

scholarly journals Construction of Deoxyriboaldolase-Overexpressing Escherichia coli and Its Application to 2-Deoxyribose 5-Phosphate Synthesis from Glucose and Acetaldehyde for 2′-Deoxyribonucleoside Production

2003 ◽  
Vol 69 (7) ◽  
pp. 3791-3797 ◽  
Author(s):  
Nobuyuki Horinouchi ◽  
Jun Ogawa ◽  
Takafumi Sakai ◽  
Takako Kawano ◽  
Seiichiro Matsumoto ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Amino Acid ◽  
Specific Activity ◽  
Cell Extract ◽  
Predicted Amino Acid Sequence ◽  
Enzymatic Reactions ◽  
Chromosomal Dna ◽  
Gene Encoding ◽  
Reading Frame ◽  
E Coli

ABSTRACT The gene encoding a deoxyriboaldolase (DERA) was cloned from the chromosomal DNA of Klebsiella pneumoniae B-4-4. This gene contains an open reading frame consisting of 780 nucleotides encoding 259 amino acid residues. The predicted amino acid sequence exhibited 94.6% homology with the sequence of DERA from Escherichia coli. The DERA of K. pneumoniae was expressed in recombinant E. coli cells, and the specific activity of the enzyme in the cell extract was as high as 2.5 U/mg, which was threefold higher than the specific activity in the K. pneumoniae cell extract. One of the E. coli transformants, 10B5/pTS8, which had a defect in alkaline phosphatase activity, was a good catalyst for 2-deoxyribose 5-phosphate (DR5P) synthesis from glyceraldehyde 3-phosphate and acetaldehyde. The E. coli cells produced DR5P from glucose and acetaldehyde in the presence of ATP. Under the optimal conditions, 100 mM DR5P was produced from 900 mM glucose, 200 mM acetaldehyde, and 100 mM ATP by the E. coli cells. The DR5P produced was further transformed to 2′-deoxyribonucleoside through coupling the enzymatic reactions of phosphopentomutase and nucleoside phosphorylase. These results indicated that production of 2′-deoxyribonucleoside from glucose, acetaldehyde, and a nucleobase is possible with the addition of a suitable energy source, such as ATP.

scholarly journals OsDOF18, A DOF Transcription Factor from Rice Confers Abiotic Stress Tolerance in Escherichia coli

2017 ◽  
Vol 60 (2) ◽  
pp. 70-79
Author(s):  
Syed Muhammad Saqlan Naqvi ◽  
Farah Deeba ◽  
Tasawar Sultana ◽  
Ghazala Kaukab Raja
Keyword(s):  
Escherichia Coli ◽  
Dna Binding ◽  
Abiotic Stresses ◽  
Abiotic Stress Tolerance ◽  
Three Dimensional ◽  
Vital Role ◽  
Dimensional Structure ◽  
Multiple Sequence ◽  
E Coli ◽  
Tolerant Plants

DNA binding with one finger proteins (DOF) play vital role in many cellular including bioticand abiotic stresses. In present study, OsDOF18, a member of DOF gene family from Oryza sativa wascloned into GST expression vector (pGEX4T-1) and sequenced. The sequence was subjected to in silicocharacterisation including similarity search, multiple sequence alignment followed by phylogenetic study.The three dimensional structure was predicted by I-TASSER server followed by authentication usingPROCHECK and QMEAN tools. Analysis of OsDOF18 by RT-qPCR confirmed the association of OsDOF18with abiotic stresses including salinity and drought. DNA binding domain containing region was clonedand over-expressed in Escherichia coli for stress analysis. OsDOF18 protein improved the E. coli survivabilityagainst salinity and drought stresses. The results suggested OsDOF18 as a stress-related gene in rice thatmay be used in generating stress tolerant plants.

scholarly journals The yiaE Gene, Located at 80.1 Minutes on the Escherichia coli Chromosome, Encodes a 2-Ketoaldonate Reductase

1998 ◽  
Vol 180 (22) ◽  
pp. 5984-5988 ◽  
Author(s):  
Do-Young Yum ◽  
Bong-Yong Lee ◽  
Dae-Hyum Hahm ◽  
Jae-Gu Pan
Keyword(s):  
Escherichia Coli ◽  
Amino Acid ◽  
Amino Acid Sequence ◽  
Metal Chelate ◽  
Reading Frame ◽  
Sequencing Project ◽  
E Coli ◽  
Dehydrogenase Gene ◽  
Translational Start

ABSTRACT An open reading frame located in the bisC-cspAintergenic region, or at 80.1 min on the Escherichia colichromosome, encodes a hypothetical 2-hydroxyacid dehydrogenase, which was identified as a result of the E. coli Genome Sequencing Project. We report here that the product of the gene (yiaE) is a 2-ketoaldonate reductase (2KR). The gene was cloned and expressed with a C-terminal His tag in E. coli, and the protein was purified by metal-chelate affinity chromatography. The determination of the NH2-terminal amino acid sequence of the protein defined the translational start site of this gene. The enzyme was found to be a 2KR catalyzing the reduction of 2,5-diketo-d-gluconate to 5-keto-d-gluconate, 2-keto-d-gluconate (2KDG) to d-gluconate, 2-keto-l-gulonate tol-idonate. The reductase was optimally active at pH 7.5, with NADPH as a preferred electron donor. The deduced amino acid sequence showed 69.4% identity with that of 2KR from Erwinia herbicola. Disruption of this gene on the chromosome resulted in the loss of 2KR activity in E. coli. E. coli W3110 was found to grow on 2KDG, whereas the mutant deficient in 2KR activity was unable to grow on 2KDG as the carbon source, suggesting that 2KR is responsible for the catabolism of 2KDG in E. coli and the diminishment of produced 2KDG from d-gluconate in the cultivation of E. coli harboring a cloned gluconate dehydrogenase gene.

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