Sequences of the Genes for the TEM-20, TEM-21, TEM-22, and TEM-29 Extended-Spectrum β-Lactamases

Merozoite surface antigen MSA-2 of the human parasite Plasmodium falciparum is being considered for the development of a malaria vaccine. The antigen is polymorphic, and specific monoclonal antibodies differentiate five serological variants of MSA-2 among 25 parasite isolates. The variants are grouped into two major serogroups, A and B. Genes encoding two different variants from serogroup A have been sequenced, and their DNA together with deduced amino acid sequences were compared with sequences encoded by other alleles. The comparison shows that the serological classification reflects differences in DNA sequences and deduced primary structure of MSA-2 variants and serogroups. Thus, the overall homologies of DNA and amino acid sequences are over 95% among variants in the same serogroup. In contrast, similarities between the group A variants and a group B variant are only 70 and 64% for DNA and amino acid sequences, respectively. We propose that the MSA-2 protein is encoded by two highly divergent groups of alleles, with limited additional polymorphism displayed within each group.

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Genes for low-molecular-weight heat shock proteins of soybeans: sequence analysis of a multigene family.

Molecular and Cellular Biology ◽

10.1128/mcb.5.12.3417 ◽

1985 ◽

Vol 5 (12) ◽

pp. 3417-3428 ◽

Cited By ~ 65

Author(s):

R T Nagao ◽

E Czarnecka ◽

W B Gurley ◽

F Schöffl ◽

J L Key

Keyword(s):

Molecular Weight ◽

Amino Acid ◽

Heat Shock ◽

Dna Sequences ◽

Regulatory Element ◽

Amino Acid Sequences ◽

Striking Similarity ◽

Low Molecular Weight ◽

Genes Encoding ◽

Flanking Regions

Soybeans, Glycine max, synthesize a family of low-molecular-weight heat shock (HS) proteins in response to HS. The DNA sequences of two genes encoding 17.5- and 17.6-kilodalton HS proteins were determined. Nuclease S1 mapping of the corresponding mRNA indicated multiple start termini at the 5' end and multiple stop termini at the 3' end. These two genes were compared with two other soybean HS genes of similar size. A comparison among the 5' flanking regions encompassing the presumptive HS promoter of the soybean HS-protein genes demonstrated this region to be extremely homologous. Analysis of the DNA sequences in the 5' flanking regions of the soybean genes with the corresponding regions of Drosophila melanogaster HS-protein genes revealed striking similarity between plants and animals in the presumptive promoter structure of thermoinducible genes. Sequences related to the Drosophila HS consensus regulatory element were found 57 to 62 base pairs 5' to the start of transcription in addition to secondary HS consensus elements located further upstream. Comparative analysis of the deduced amino acid sequences of four soybean HS proteins illustrated that these proteins were greater than 90% homologous. Comparison of the amino acid sequence for soybean HS proteins with other organisms showed much lower homology (less than 20%). Hydropathy profiles for Drosophila, Xenopus, Caenorhabditis elegans, and G. max HS proteins showed a similarity of major hydrophilic and hydrophobic regions, which suggests conservation of functional domains for these proteins among widely dispersed organisms.

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The variable subunit associated with protein phosphatase 2A0 defines a novel multimember family of regulatory subunits

Biochemical Journal ◽

10.1042/bj3170187 ◽

1996 ◽

Vol 317 (1) ◽

pp. 187-194 ◽

Cited By ~ 55

Author(s):

Stanislaw ZOLNIEROWICZ ◽

Christine VAN HOOF ◽

Nataša ANDJELKOVIĆ ◽

Peter CRON ◽

Ilse STEVENS ◽

...

Keyword(s):

Amino Acid ◽

Protein Phosphatase ◽

Amino Acid Sequences ◽

Regulatory Subunits ◽

Consensus Sequences ◽

Reverse Transcription Pcr ◽

Genes Encoding ◽

Phosphatase 2A ◽

Molecular Masses ◽

Specific Mrnas

Two protein phosphatase 2A (PP2A) holoenzymes were isolated from rabbit skeletal muscle containing, in addition to the catalytic and PR65 regulatory subunits, proteins of apparent molecular masses of 61 and 56 kDa respectively. Both holoenzymes displayed low basal phosphorylase phosphatase activity, which could be stimulated by protamine to an extent similar to that of previously characterized PP2A holoenzymes. Protein microsequencing of tryptic peptides derived from the 61 kDa protein, termed PR61, yielded 117 residues of amino acid sequence. Molecular cloning by enrichment of specific mRNAs, followed by reverse transcription–PCR and cDNA library screening, revealed that this protein exists in multiple isoforms encoded by at least three genes, one of which gives rise to several splicing variants. Comparisons of these sequences with the available databases identified one more human gene and predicted another based on a rabbit cDNA-derived sequence, thus bringing the number of genes encoding PR61 family members to five. Peptide sequences derived from PR61 corresponded to the deduced amino acid sequences of either α or β isoforms, indicating that the purified PP2A preparation was a mixture of at least two trimers. In contrast, the 56 kDa subunit (termed PR56) seems to correspond to the ϵ isoform of PR61. Several regulatory subunits of PP2A belonging to the PR61 family contain consensus sequences for nuclear localization and might therefore target PP2A to nuclear substrates.

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Structural and antigenic polymorphism of the 35- to 48-kilodalton merozoite surface antigen (MSA-2) of the malaria parasite Plasmodium falciparum.

Molecular and Cellular Biology ◽

10.1128/mcb.11.2.963 ◽

1991 ◽

Vol 11 (2) ◽

pp. 963-971 ◽

Cited By ~ 98

Author(s):

B Fenton ◽

J T Clark ◽

C M Khan ◽

J V Robinson ◽

D Walliker ◽

...

Keyword(s):

Plasmodium Falciparum ◽

Amino Acid ◽

Surface Antigen ◽

Dna Sequences ◽

Amino Acid Sequences ◽

Merozoite Surface Antigen ◽

Parasite Plasmodium ◽

Genes Encoding ◽

Parasite Plasmodium Falciparum ◽

Group B

Merozoite surface antigen MSA-2 of the human parasite Plasmodium falciparum is being considered for the development of a malaria vaccine. The antigen is polymorphic, and specific monoclonal antibodies differentiate five serological variants of MSA-2 among 25 parasite isolates. The variants are grouped into two major serogroups, A and B. Genes encoding two different variants from serogroup A have been sequenced, and their DNA together with deduced amino acid sequences were compared with sequences encoded by other alleles. The comparison shows that the serological classification reflects differences in DNA sequences and deduced primary structure of MSA-2 variants and serogroups. Thus, the overall homologies of DNA and amino acid sequences are over 95% among variants in the same serogroup. In contrast, similarities between the group A variants and a group B variant are only 70 and 64% for DNA and amino acid sequences, respectively. We propose that the MSA-2 protein is encoded by two highly divergent groups of alleles, with limited additional polymorphism displayed within each group.

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Fluoroquinolone resistance in Clostridium difficile isolates from a prospective study of C. difficile infections in Europe

Journal of Medical Microbiology ◽

10.1099/jmm.0.47738-0 ◽

2008 ◽

Vol 57 (6) ◽

pp. 784-789 ◽

Cited By ~ 85

Author(s):

Patrizia Spigaglia ◽

Fabrizio Barbanti ◽

Paola Mastrantonio ◽

Jon S. Brazier ◽

Frédéric Barbut ◽

...

Keyword(s):

Amino Acid ◽

Clostridium Difficile ◽

Prospective Study ◽

Amino Acid Substitution ◽

Amino Acid Change ◽

Fluoroquinolone Resistance ◽

Genes Encoding ◽

High Level ◽

A Prospective Study

The European Study Group on Clostridium difficile (ESGCD) conducted a prospective study in 2005 to monitor and characterize C. difficile strains circulating in European hospitals, collecting 411 isolates. Eighty-three of these isolates, showing resistance or intermediate resistance to moxifloxacin (MX), were selected for this study to assess susceptibility to other fluoroquinolones (FQs) and to analyse the gyr genes, encoding the DNA gyrase subunits GyrA and GyrB. Twenty MX-susceptible isolates from the surveillance study were included for comparison. Overall, one amino acid substitution in GyrA (Thr82 to Ile) and four different substitutions in GyrB (Ser416 to Ala, Asp426 to Asn, Asp426 to Val and Arg447 to Lys) were identified. A high level of resistance (MIC ≥32 μg ml−1) to MX, ciprofloxacin (CI), gatifloxacin (GA) and levofloxacin (LE) was found in 68 isolates showing the amino acid substitution Thr82 to Ile in GyrA, in eight isolates with the substitutions Thr82 to Ile in GyrA and Ser416 to Ala in GyrB, in two isolates showing the substitution Asp426 to Asn in GyrB and in one isolate with Asp426 to Val in GyrB. The remaining four isolates showed high MICs for CI and LE, but different MIC levels for MX and GA. In particular, intermediate levels of resistance to MX were shown by two isolates, one with the substitution Thr82 to Ile in GyrA, and one showing Asp426 to Asn in GyrB. The substitution Arg447 to Lys in GyrB was found in two strains resistant to MX, CI and LE but susceptible to GA. No substitutions in GyrA were found in the FQ-susceptible strains, whereas two strains showed the amino acid change Ser416 to Ala in GyrB. Thr82 to Ile was the most frequent amino acid change identified in the C. difficile isolates examined. In contrast to previous observations, 10 % of the isolates showed this substitution in association with Ser416 to Ala in GyrB. The other amino acid changes found were characteristic of a few strains belonging to certain types and/or countries. Two new substitutions for C. difficile, Ser416 to Ala and Arg447 to Lys, were found in GyrB. Whereas the former does not seem to have a key role in resistance, since it was also detected in susceptible strains, the latter substitution occurred in the same position where other amino acid variations take place in resistant Escherichia coli and other C. difficile strains. A large number of C. difficile isolates now show an alarming pattern of resistance to the majority of FQs currently used in hospitals and outpatient settings, therefore judicious use of these antibiotics and continuous monitoring of in vitro resistance are necessary.

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Characterization of Novel Carbazole Catabolism Genes from Gram-Positive Carbazole Degrader Nocardioides aromaticivorans IC177

Applied and Environmental Microbiology ◽

10.1128/aem.72.5.3321-3329.2006 ◽

2006 ◽

Vol 72 (5) ◽

pp. 3321-3329 ◽

Cited By ~ 40

Author(s):

Kengo Inoue ◽

Hiroshi Habe ◽

Hisakazu Yamane ◽

Hideaki Nojiri

Keyword(s):

Amino Acid ◽

Gene Clusters ◽

Amino Acid Sequences ◽

Open Reading Frames ◽

Class Iii ◽

Rt Pcr ◽

Gram Positive ◽

Mononuclear Iron ◽

Reverse Transcription Pcr ◽

Genes Encoding

ABSTRACT Nocardioides aromaticivorans IC177 is a gram-positive carbazole degrader. The genes encoding carbazole degradation (car genes) were cloned into a cosmid clone and sequenced partially to reveal 19 open reading frames. The car genes were clustered into the carAaCBaBbAcAd and carDFE gene clusters, encoding the enzymes responsible for the degradation of carbazole to anthranilate and 2-hydroxypenta-2,4-dienoate and of 2-hydroxypenta-2,4-dienoate to pyruvic acid and acetyl coenzyme A, respectively. The conserved amino acid motifs proposed to bind the Rieske-type [2Fe-2S] cluster and mononuclear iron, the Rieske-type [2Fe-2S] cluster, and flavin adenine dinucleotide were found in the deduced amino acid sequences of carAa, carAc, and carAd, respectively, which showed similarities with CarAa from Sphingomonas sp. strain KA1 (49% identity), CarAc from Pseudomonas resinovorans CA10 (31% identity), and AhdA4 from Sphingomonas sp. strain P2 (37% identity), respectively. Escherichia coli cells expressing CarAaAcAd exhibited major carbazole 1,9a-dioxygenase (CARDO) activity. These data showed that the IC177 CARDO is classified into class IIB, while gram-negative CARDOs are classified into class III or IIA, indicating that the respective CARDOs have diverse types of electron transfer components and high similarities of the terminal oxygenase. Reverse transcription-PCR (RT-PCR) experiments showed that the carAaCBaBbAcAd and carDFE gene clusters are operonic. The results of quantitative RT-PCR experiments indicated that transcription of both operons is induced by carbazole or its metabolite, whereas anthranilate is not an inducer. Biotransformation analysis showed that the IC177 CARDO exhibits significant activities for naphthalene, carbazole, and dibenzo-p-dioxin but less activity for dibenzofuran and biphenyl.

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Nucleotide and deduced amino acid sequences of genes encoding the structural and nonstructural NS1 proteins of a dengue-2 virus isolated in China

Virus Genes ◽

10.1007/bf01703603 ◽

1994 ◽

Vol 8 (1) ◽

pp. 71-74 ◽

Cited By ~ 3

Author(s):

Pei-Ying Yang ◽

Ingrid Kautner ◽

Chong-Lek Koh ◽

Sai-Kit Lam

Keyword(s):

Amino Acid ◽

Amino Acid Sequences ◽

Genes Encoding

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An optimized FM-index library for nucleotide and amino acid search

Algorithms for Molecular Biology ◽

10.1186/s13015-021-00204-6 ◽

2021 ◽

Vol 16 (1) ◽

Author(s):

Tim Anderson ◽

Travis J. Wheeler

Keyword(s):

Amino Acid ◽

Open Source ◽

Pattern Matching ◽

Suffix Array ◽

Amino Acid Sequences ◽

Lookup Table ◽

Efficient Computation ◽

Biological Sequence ◽

Run Time ◽

High Level

Abstract Background Pattern matching is a key step in a variety of biological sequence analysis pipelines. The FM-index is a compressed data structure for pattern matching, with search run time that is independent of the length of the database text. Implementation of the FM-index is reasonably complicated, so that increased adoption will be aided by the availability of a fast and flexible FM-index library. Results We present AvxWindowedFMindex (AWFM-index), a lightweight, open-source, thread-parallel FM-index library written in C that is optimized for indexing nucleotide and amino acid sequences. AWFM-index introduces a new approach to storing FM-index data in a strided bit-vector format that enables extremely efficient computation of the FM-index occurrence function via AVX2 bitwise instructions, and combines this with optional on-disk storage of the index’s suffix array and a cache-efficient lookup table for partial k-mer searches. The AWFM-index performs exact match count and locate queries faster than SeqAn3’s FM-index implementation across a range of comparable memory footprints. When optimized for speed, AWFM-index is $$\sim $$ ∼ 2–4x faster than SeqAn3 for nucleotide search, and $$\sim $$ ∼ 2–6x faster for amino acid search; it is also $$\sim $$ ∼ 4x faster with similar memory footprint when storing the suffix array in on-disk SSD storage. Conclusions AWFM-index is easy to incorporate into bioinformatics software, offers run-time performance parameterization, and provides clients with FM-index functionality at both a high-level (count or locate all instances of a query string) and low-level (step-wise control of the FM-index backward-search process). The open-source library is available for download at https://github.com/TravisWheelerLab/AvxWindowFmIndex.

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The role of synonymous mutations in the evolution of TEM β-lactamase genes

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00018-21 ◽

2021 ◽

Author(s):

Mohammad Faheem ◽

Charles J. Zhang ◽

Monica N. Morris ◽

Juergen Pleiss ◽

Peter Oelschlaeger

Keyword(s):

Escherichia Coli ◽

Amino Acid ◽

Disc Diffusion ◽

Nucleotide Change ◽

Nonsynonymous Mutation ◽

Synonymous Mutations ◽

Extended Spectrum ◽

Genes Encoding ◽

Variant Genes

Nonsynonymous mutations are well documented in TEM β-lactamases. The resulting amino acid changes often alter the conferred phenotype from broad spectrum (2b) conferred by TEM-1 to extended spectrum (2be), inhibitor resistant (2br), or both extended spectrum and inhibitor resistant (2ber). The encoding blaTEM genes also deviate in numerous synonymous mutations, which are not well understood. blaTEM-3 (2be), blaTEM-33 (2br), and blaTEM-109 (2ber) were studied in comparison to blaTEM-1. blaTEM-33 was chosen for more detailed studies, because it deviates from blaTEM-1 by a single nonsynonymous mutation and three additional, synonymous mutations. Genes encoding the enzymes with only nonsynonymous or all, including synonymous, mutations plus all permutations between blaTEM-1 and blaTEM-33 were expressed in Escherichia coli cells. In disc diffusion assays, genes encoding TEM-3, TEM-33, and TEM-109 with all synonymous mutations resulted in higher resistance levels than genes without synonymous mutations. Disc diffusion assays with the 16 genes carrying all possible nucleotide change combinations between blaTEM-1 and blaTEM-33 indicated different susceptibilities for different variants. Nucleotide BLAST searches did not identify genes without synonymous mutations but some without nonsynonymous mutations. Energies of possible secondary mRNA structures calculated with mfold are generally higher with synonymous mutations, suggesting that their role could be to destabilize the mRNA and facilitate its unfolding for efficient translation. In summary, our data indicate that transitions from blaTEM-1 to other variant genes by simply acquiring the nonsynonymous mutations is not favored. Instead, synonymous mutations seem to support the transition to other variant genes with nonsynonymous mutations leading to different phenotypes.

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