scholarly journals Species and Metabolic Pathways Involved in Bioremediation of Vietnamese Soil From Bien Hoa Airbase Contaminated With Herbicides

2021 ◽  
Vol 3 ◽  
Author(s):  
Thi Lan Anh Nguyen ◽  
Ha Thi Cam Dang ◽  
Jacco Koekkoek ◽  
Martin Braster ◽  
John R. Parsons ◽  
...  
Keyword(s):  
Amino Acid ◽  
Genomic Analysis ◽  
Dry Weight ◽  
Gene Organization ◽  
Amino Acid Sequences ◽  
Achromobacter Xylosoxidans ◽  
Type I ◽  
Gene Products ◽  
Bacterial Strains ◽  
Full Complement

Four bacterial strains were isolated from enrichment cultures inoculated with soil from Bien Hoa military base in Vietnam contaminated with the herbicides 2,4-dichlorophenoxyacetate (2,4-D) and 2,4,5-trichlorophenoxyacetate (2,4,5-T). They were classified as Pseudomonas aeruginosa BT1 2.2, Sphingomonas histidinilytica BT1 5.2, Bordetella petrii BT1 9.2, and Achromobacter xylosoxidans BT1 10.2. All four were able to degrade 2,4-D and 2,4,5-T, but only the last three species used them as the sole sources of carbon and energy. Mass balance analyses suggest that between 33 and 46% of the carbon in the herbicides is incorporated into dry weight (DW). We obtained insight into their degradation pathways by the genomic analysis of these strains. A tfdCDEF gene cluster was found in A. xylosoxidans BT1 10.2 with amino acid sequences of their gene products showing high identity to those in B. petrii DSM12804. Bordetella petrii BT1 9.2 has a full complement of the tfdABCDEF genes. Surprisingly, the gene organization along with the amino acid sequences of the gene products are virtually identical to those of Cupriavidus pinatubonensis JMP134, referred to as type I tfd genes, and different from those of A. xylosoxidans BT1 10.2 and B. petrii DSM12804. We hypothesize that some of the genetic potential to degrade the herbicides has been recruited in recent mating events between these species and other members of the proteobacteria. This is the first report showing that B. petrii BT1 9.2 emerges as a key player in the degradation of 2,4-D.

Diversity within the Campylobacter jejuni type I restriction–modification loci

Microbiology ◽  
2005 ◽  
Vol 151 (2) ◽  
pp. 337-351 ◽  
Author(s):  
William G. Miller ◽  
Bruce M. Pearson ◽  
Jerry M. Wells ◽  
Craig T. Parker ◽  
Vladimir V. Kapitonov ◽  
...  
Keyword(s):  
Amino Acid ◽  
Campylobacter Jejuni ◽  
Gene Organization ◽  
Nucleotide Sequences ◽  
Amino Acid Sequences ◽  
Type I ◽  
New Genes ◽  
Or Gene ◽  
H Pylori ◽  
Restriction Modification

The type I restriction–modification (hsd) systems of 73 Campylobacter jejuni strains were characterized according to their DNA and amino acid sequences, and/or gene organization. A number of new genes were identified which are not present in the sequenced strain NCTC 11168. The closely related organism Helicobacter pylori has three type I systems; however, no evidence was found that C. jejuni strains contain multiple type I systems, although hsd loci are present in at least two different chromosomal locations. Also, unlike H. pylori, intervening ORFs are present, in some strains, between hsdR and hsdS and between hsdS and hsdM. No definitive function can be ascribed to these ORFs, designated here as rloA–H (R-linked ORF) and mloA–B (M-linked ORF). Based on parsimony analysis of amino acid sequences to assess character relatedness, the C. jejuni type I R–M systems are assigned to one of three families: ‘IAB’, ‘IC’ or ‘IF’. This study confirms that HsdM proteins within a family are highly conserved but share little homology with HsdM proteins from other families. The ‘IC’ hsd loci are >99 % identical at the nucleotide level, as are the ‘IF’ hsd loci. Additionally, whereas the nucleotide sequences of the ‘IAB’ hsdR and hsdM genes show a high degree of similarity, the nucleotide sequences of the ‘IAB’ hsdS and rlo genes vary considerably. This diversity suggests that recombination between ‘IAB’ hsd loci would lead not only to new hsdS alleles but also to the exchange of rlo genes; five C. jejuni hsd loci are presumably the result of such recombination. The importance of these findings with regard to the evolution of C. jejuni type I R–M systems is discussed.

scholarly journals Molecular Analysis of Resistance to Streptogramin A Compounds Conferred by the Vga Proteins of Staphylococci

2005 ◽  
Vol 49 (3) ◽  
pp. 973-980 ◽  
Author(s):  
Olivier Chesneau ◽  
Heidi Ligeret ◽  
Negin Hosan-Aghaie ◽  
Anne Morvan ◽  
Elie Dassa
Keyword(s):  
Antibiotic Resistance ◽  
Amino Acid ◽  
Sequence Analysis ◽  
Polyclonal Antibodies ◽  
Amino Acid Sequences ◽  
Gene Products ◽  
Β Subunit ◽  
Abc Proteins ◽  
Gram Positive Bacteria ◽  
Resistance Determinants

ABSTRACT The Vga and Msr resistance determinants, encoded by mobile genetic elements in various staphylococcal strains, belong to a family of ATP-binding cassette (ABC) proteins whose functions and structures are ill defined. Their amino acid sequences are similar to those of proteins involved in the immunity of streptomycetes to the macrolide-lincosamide-streptogramin antibiotics that they produce. Sequence analysis of the genomes of the gram-positive bacteria with low G+C contents revealed that Lmo0919 from Listeria monocytogenes is more closely related to Vga variants than to Msr variants. In the present study we compared the antibiotic resistance profiles conferred by the Vga-like proteins in two staphylococcal hosts. It was shown that Vga(A), the Vga(A) variant [Vga(A)v], and Lmo0919 can confer resistance to lincosamides and streptogramin A compounds, while only Vga(B) is able to increase the level of resistance to pristinamycin, a mixture of streptogramin A and streptogramin B compounds. By using polyclonal antibodies, we found that the Vga(A) protein colocalized with the β subunit of the F1-F0 ATPase in the membrane fractions of staphylococcal cells. In order to identify functional units in these atypical ABC proteins, such as regions that might be involved in substrate specificity and/or membrane targeting, we analyzed the resistance phenotypes conferred by various plasmids carrying parts or modified versions of the vga(A) gene and we determined the subcellular localization of the gene products. Only polypeptides composed of two ABC domains were detected in the cell membranes. No region of drug specificity was identified. Resistance properties were dependent on the integrities of both Walker B motifs.

scholarly journals Specificities of IncF plasmid conjugation genes

1986 ◽  
Vol 47 (1) ◽  
pp. 1-11 ◽  
Author(s):  
Neil Willetts ◽  
John Maule
Keyword(s):  
Amino Acid ◽  
Recipient Cell ◽  
Amino Acid Sequences ◽  
Evolutionary Relationships ◽  
Gene Products ◽  
Dna Homology ◽  
Primary Amino ◽  
Acting In Concert ◽  
Surface Exclusion ◽  
Plasmid Conjugation

SummaryThe conjugation regions of IncF plasmids are closely related in that they share extensive DNA homology, and that they specify related pili. Variations between individual conjugation gene products of different IncF plasmids have, however, been noted. We have extended these observations by carrying out a systematic survey of twelve such plasmids, to examine the numbers and the groupings of the plasmid-specific alleles of several genes required for conjugation and its control.Using vector plasmids carrying cloned origins of transfer (oriT), four different specificities were recognized, and these were correlated with the specificities of the genes with products that may act at this site (traM, traYandtraZ). ThetraYgene is the first gene of the major transfer operon, and is therefore located close to the site at which thetraJprotein acts to induce expression of the operon: correspondingly, correlation was observed between theoriT/traMYZandtraJspecificities in most of the plasmids. In turn,traJis negatively regulated by thefinOandfinPproducts acting in concert: thefinOproduct was relatively non-specific, but sixfinPalleles were identified, again with specificities correlated with those oftraJ. Our explanation for this unexpectedly large number offinPalleles derives from the concept that thefinPproduct is an RNA molecule rather than a protein. Although the conjugative pili encoded by IncF plasmids are closely related, they confer different efficiencies of plating of the various F-specific bacteriophages. We distinguished four groups on this basis, presumably resulting from differences in the primary amino-acid sequences of the pilin proteins. These groups could be related to the surface exclusion system specificities, consistent with the hypothesis that surface exclusion acts at least in part by preventing interaction between the pilus and the recipient cell surface.From these data, information about the evolutionary relationships between the twelve IncF plasmids can be deduced.

scholarly journals The two alpha-tubulin genes of Chlamydomonas reinhardi code for slightly different proteins.

1985 ◽  
Vol 5 (9) ◽  
pp. 2389-2398 ◽  
Author(s):  
C D Silflow ◽  
R L Chisholm ◽  
T W Conner ◽  
L P Ranum
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequences ◽  
Cdna Clones ◽  
Gene Products ◽  
Beta Tubulin ◽  
Alpha Tubulin ◽  
Tubulin Genes ◽  
Total Complement ◽  
Cloned Gene ◽  
Net Charges

Full-length cDNA clones corresponding to the transcripts of the two alpha-tubulin genes in Chlamydomonas reinhardi were isolated. DNA sequence analysis of the cDNA clones and cloned gene fragments showed that each gene contains 1,356 base pairs of coding sequence, predicting alpha-tubulin products of 451 amino acids. Of the 27 nucleotide differences between the two genes, only two result in predicted amino acid differences between the two gene products. In the more divergent alpha 2 gene, a leucine replaces an arginine at amino acid 308, and a valine replaces a glycine at amino acid 366. The results predicted that two alpha-tubulin proteins with different net charges are produced as primary gene products. The predicted amino acid sequences are 86 and 70% homologous with alpha-tubulins from rat brain and Schizosaccharomyces pombe, respectively. Each gene had two intervening sequences, located at identical positions. Portions of an intervening sequence highly conserved between the two beta-tubulin genes are also found in the second intervening sequence of each of the alpha genes. These results, together with our earlier report of the beta-tubulin sequences in C. reinhardi, present a picture of the total complement of genetic information for tubulin in this organism.

scholarly journals Amino acid sequences of α-helical segments from S-carboxymethylkerateine-A. Complete sequence of a type-II segment

1978 ◽  
Vol 173 (2) ◽  
pp. 365-371 ◽  
Author(s):  
W G Crewther ◽  
A S Inglis ◽  
N M McKern
Keyword(s):  
Amino Acid ◽  
Coiled Coil ◽  
Complete Sequence ◽  
Amino Acid Sequences ◽  
Helical Axis ◽  
Type I ◽  
Type Ii ◽  
Coil Structure ◽  
Aqueous Urea ◽  
Alpha Keratin

1. The helical fragments obtained by partial chymotryptic digestion of S-carboxymethylkeratine-A, the low-sulphur fraction from wool, were fractionated into type-I and type-II helical segments in aqueous urea under conditions limiting carbamoylation. 2. The amino acid sequence of a 109-residue type-II segment was completed by using the sequenator. 3. When the data were incorporated into a helical model of 3.6 residues per turn the hydrophobic residues generated a band aligned at a slight angle to the helical axis. This result is in accord with the postulated coiled-coil structure of the crystalline regions of alpha-keratin.

Expression and Regulation of the Arsenic Resistance Operon of Acidiphilium multivorum AIU 301 Plasmid pKW301 in Escherichia coli

1998 ◽  
Vol 64 (2) ◽  
pp. 411-418 ◽  
Author(s):  
Katsuhisa Suzuki ◽  
Norio Wakao ◽  
Tetsuya Kimura ◽  
Kazuo Sakka ◽  
Kunio Ohmiya
Keyword(s):  
Escherichia Coli ◽  
Amino Acid ◽  
Constitutive Expression ◽  
Amino Acid Sequences ◽  
Gene Products ◽  
Arsenic Resistance ◽  
E Coli ◽  
Molecular Weights ◽  
Rna Polymerase Promoter ◽  
Extension Analysis

ABSTRACT The arsenic resistance (ars) operon from plasmid pKW301 of Acidiphilium multivorum AIU 301 was cloned and sequenced. This DNA sequence contains five genes in the following order: arsR, arsD, arsA,arsB, arsC. The predicted amino acid sequences of all of the gene products are homologous to the amino acid sequences of the ars gene products of Escherichia coliplasmid R773 and IncN plasmid R46. The ars operon cloned from A. multivorum conferred resistance to arsenate and arsenite on E. coli. Expression of the arsgenes with the bacteriophage T7 RNA polymerase-promoter system allowedE. coli to overexpress ArsD, ArsA, and ArsC but not ArsR or ArsB. The apparent molecular weights of ArsD, ArsA, and ArsC were 13,000, 64,000, and 16,000, respectively. A primer extension analysis showed that the ars mRNA started at a position 19 nucleotides upstream from the arsR ATG in E. coli. Although the arsR gene of A. multivorum AIU 301 encodes a polypeptide of 84 amino acids that is smaller and less homologous than any of the other ArsR proteins, inactivation of the arsR gene resulted in constitutive expression of the ars genes, suggesting that ArsR of pKW301 controls the expression of this operon.

DNA sequence analysis of a mouse pro alpha 1 (I) procollagen gene: evidence for a mouse B1 element within the gene

1982 ◽  
Vol 2 (11) ◽  
pp. 1362-1371
Author(s):  
J M Monson ◽  
J Friedman ◽  
B J McCarthy
Keyword(s):  
Amino Acid ◽  
Dna Sequence ◽  
Repetitive Sequences ◽  
Rna Polymerase Iii ◽  
Amino Acid Sequences ◽  
Type I ◽  
Base Pairs ◽  
Coding Sequences ◽  
Splice Junctions ◽  
I Gene

In a 3.8-kilobase mouse DNA sequence encoding amino acid sequences for the pro alpha 1(I) chain of type I procollagen, 14 coding sequences were identified which specify a sequence 95% homologous to amino acid residues 568 to 963 of the bovine alpha 1(I) chain. All of these coding sequences were flanked by appropriate splice junctions following the GT/AG rule. These observations suggest, but do not prove, that this pro alpha 1(I) gene is transcriptionally active. Of the 14 coding sequences, 7 were 54 base pairs in length, whereas the remainder were higher multiples of 54 base pairs. Nonrandom utilization of codons pertained throughout all of the coding sequences showing a preference (56%) for U in the wobble position. Two of the intervening sequences encoded imperfect vestiges of coding sequences which exhibited a codon preference different from that of the pro alpha 1(I) gene proper and were not flanked by splice junctions. One intervening sequence encoded a member of the mouse B1 family of middle repetitive sequences. It was flanked by 8-base-pair direct repeats and had a truncated A-rich region, suggesting that it may be a mobile element. Within this element were sequences which could function as a RNA polymerase III split promoter.

scholarly journals Amino acid sequences of α-helical segments from S-carbosymethylkerateine-A. Complete sequence of a type-I segment

1978 ◽  
Vol 173 (2) ◽  
pp. 373-385 ◽  
Author(s):  
K H Gough ◽  
A S Inglis ◽  
W G Crewther
Keyword(s):  
Amino Acid ◽  
Sequence Data ◽  
Coiled Coil ◽  
Alpha Helix ◽  
Protein S ◽  
Amino Acid Sequences ◽  
Type I ◽  
Type Ii ◽  
Sequencing Data ◽  
Helical Segment

The amino acid sequence of a type-I helical segment from the low-sulphur protein (S-carboxymethylkerateine-A) of wool was determined by combining automatic and manual-sequencing data. Whereas in the type-II helical segment most of the cationic groups occur in pairs, 11 of the 22 anionic residues in the sequence of the type-I segment were situated next to a second anionic residue. This suggests possible interactions between type-I and type-II helical segments in alpha-keratin. As observed with the sequence of a type-II helical segment a model constructed on 3.6 residues per turn of helix shows a line of hydrophobic residues along the helix, thereby supporting the physicochemical evidence that the molecule is predominantly helical and forms part of a coiled-coil structure. Examination of the sequence data by predictive methods indicates the possibilty of extensive sections of alpha-helix interspersed with discontinuities. The molecule contains a number of regions with peptide sequences identical with those found by other workers after enzymic digestion of fractions from oxidized wool.

scholarly journals Localization and Characterization of Two Novel Genes Encoding Stereospecific Dioxygenases Catalyzing 2(2,4-Dichlorophenoxy)propionate Cleavage in Delftia acidovorans MC1

2004 ◽  
Vol 70 (9) ◽  
pp. 5357-5365 ◽  
Author(s):  
Kathleen M. Schleinitz ◽  
Sabine Kleinsteuber ◽  
Tatiana Vallaeys ◽  
Wolfgang Babel
Keyword(s):  
Amino Acid ◽  
Ralstonia Eutropha ◽  
Single Copy ◽  
Amino Acid Sequences ◽  
Sequence Motif ◽  
Bacterial Strains ◽  
Novel Genes ◽  
Delftia Acidovorans ◽  
Important Amino Acid ◽  
Genes Encoding

ABSTRACT Two novel genes, rdpA and sdpA, encoding the enantiospecific α-ketoglutarate dependent dioxygenases catalyzing R,S-dichlorprop cleavage in Delftia acidovorans MC1 were identified. Significant similarities to other known genes were not detected, but their deduced amino acid sequences were similar to those of other α-ketoglutarate dioxygenases. RdpA showed 35% identity with TauD of Pseudomonas aeruginosa, and SdpA showed 37% identity with TfdA of Ralstonia eutropha JMP134. The functionally important amino acid sequence motif HX(D/E)X23-26(T/S)X114-183HX10-13R/K, which is highly conserved in group II α-ketoglutarate-dependent dioxygenases, was present in both dichlorprop-cleaving enzymes. Transposon mutagenesis of rdpA inactivated R-dichlorprop cleavage, indicating that it was a single-copy gene. Both rdpA and sdpA were located on the plasmid pMC1 that also carries the lower pathway genes. Sequencing of a 25.8-kb fragment showed that the dioxygenase genes were separated by a 13.6-kb region mainly comprising a Tn501-like transposon. Furthermore, two copies of a sequence similar to IS91-like elements were identified. Hybridization studies comparing the wild-type plasmid and that of the mutant unable to cleave dichlorprop showed that rdpA and sdpA were deleted, whereas the lower pathway genes were unaffected, and that deletion may be caused by genetic rearrangements of the IS91-like elements. Two other dichlorprop-degrading bacterial strains, Rhodoferax sp. strain P230 and Sphingobium herbicidovorans MH, were shown to carry rdpA genes of high similarity to rdpA from strain MC1, but sdpA was not detected. This suggested that rdpA gene products are involved in the degradation of R-dichlorprop in these strains.

scholarly journals Characterization of Martelella soudanensis sp. nov., Isolated from a Mine Sediment

2021 ◽  
Vol 9 (8) ◽  
pp. 1736
Author(s):  
Jung-Yun Lee ◽  
Dong-Hun Lee ◽  
Dong-Hun Kim
Keyword(s):  
Amino Acid ◽  
Genomic Analysis ◽  
Amino Acid Identity ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
General Function ◽  
Bacterial Strains ◽  
Respiratory Quinone ◽  
Average Amino Acid Identity ◽  
Iron Mine

Gram-stain-negative, strictly aerobic, non-spore-forming, non-motile, and rod-shaped bacterial strains, designated NC18T and NC20, were isolated from the sediment near-vertical borehole effluent originating 714 m below the subsurface located in the Soudan Iron Mine in Minnesota, USA. The 16S rRNA gene sequence showed that strains NC18T and NC20 grouped with members of the genus Martelella, including M. mediterranea DSM 17316T and M. limonii YC7034T. The genome sizes and G + C content of both NC18T and NC20 were 6.1 Mb and 61.8 mol%, respectively. Average nucleotide identity (ANI), the average amino acid identity (AAI), and digital DNA–DNA hybridization (dDDH) values were below the species delineation threshold. Pan-genomic analysis showed that NC18T, NC20, M. mediterranea DSM 17316T, M. endophytica YC6887T, and M. lutilitoris GH2-6T had 8470 pan-genome orthologous groups (POGs) in total. Five Martelella strains shared 2258 POG core, which were mainly associated with amino acid transport and metabolism, general function prediction only, carbohydrate transport and metabolism, translation, ribosomal structure and biogenesis, and transcription. The two novel strains had major fatty acids (>5%) including summed feature 8 (C18:1 ω7c and/or C18:1 ω6c), C19:0 cyclo ω8c, C16:0, C18:1 ω7c 11-methyl, C18:0, and summed feature 2 (C12:0 aldehyde and/or iso-C16:1 I and/or C14:0 3-OH). The sole respiratory quinone was uniquinone-10 (Q-10). On the basis of polyphasic taxonomic analyses, strains NC18T and NC20 represent novel species of the genus Martelella, for which the name Martelella soudanensis sp. nov. is proposed. The type strain is NC18T (=KTCT 82174T = NBRC 114661T).

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