Genetic variability of the M genome segment of clinical and environmental Toscana virus strains

Twenty-seven strains of Toscana virus, collected over a period of 23 years and isolated from several localities and from different hosts (humans, arthropods and a bat), were investigated by sequencing of a portion of the M genomic segment comprising the GN glycoprotein coding region. Sequence data indicated that the divergence among isolates ranged from 0 to 5.7 % at the nucleotide level and from 0 to 3.4 % at the amino acid level. Phylogenetic analysis revealed four main clusters. A close correspondence between viral strains and area/year of isolation could not be demonstrated, whilst co-circulation of different viral strains in the same area and in the same time period was observed for both patients and environmental viral isolates. Alignment of the deduced amino acid sequences and evolutionary analysis indicated that most of the sites along the gene may be invariable because of purifying and/or neutral selection.

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Murine erythropoietin gene: cloning, expression, and human gene homology.

Molecular and Cellular Biology ◽

10.1128/mcb.6.3.849 ◽

1986 ◽

Vol 6 (3) ◽

pp. 849-858 ◽

Cited By ~ 131

Author(s):

C B Shoemaker ◽

L D Mitsock

Keyword(s):

Amino Acid ◽

Genomic Library ◽

Cdna Probe ◽

Amino Acid Sequences ◽

Nucleotide Sequence Analysis ◽

Coding Region ◽

Transcription Control ◽

Erythroid Progenitor ◽

Human Genes ◽

Cell Expression

The gene for murine erythropoietin (EPO) was isolated from a mouse genomic library with a human EPO cDNA probe. Nucleotide sequence analysis permitted the identification of the murine EPO coding sequence and the prediction of the encoded amino acid sequence based on sequence conservation between the mouse and human EPO genes. Both the coding DNA and the amino acid sequences were 80% conserved between the two species. Transformation of COS-1 cells with a mammalian cell expression vector containing the murine EPO coding region resulted in secretion of murine EPO with biological activity on both murine and human erythroid progenitor cells. The transcription start site for the murine EPO gene in kidneys was determined. This permitted tentative identification of the transcription control region. The region included 140 base pairs upstream of the cap site which was over 90% conserved between the murine and human genes. Surprisingly, the first intron and much of the 5'- and 3'-untranslated sequences were also substantially conserved between the genes of the two species.

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Techniques for the verification of minimal phylogenetic trees illustrated with ten mammalian haemoglobin sequences

Biochemical Journal ◽

10.1042/bj1870065 ◽

1980 ◽

Vol 187 (1) ◽

pp. 65-74 ◽

Cited By ~ 12

Author(s):

D Penny ◽

M D Hendy ◽

L R Foulds

Keyword(s):

Amino Acid ◽

Phylogenetic Tree ◽

Protein Sequence ◽

Phylogenetic Trees ◽

Sequence Data ◽

Protein Sequences ◽

Nucleotide Sequences ◽

Amino Acid Sequences ◽

Minimal Tree ◽

Protein Sequence Data

We have recently reported a method to identify the shortest possible phylogenetic tree for a set of protein sequences [Foulds Hendy & Penny (1979) J. Mol. Evol. 13. 127–150; Foulds, Penny & Hendy (1979) J. Mol. Evol. 13, 151–166]. The present paper discusses issues that arise during the construction of minimal phylogenetic trees from protein-sequence data. The conversion of the data from amino acid sequences into nucleotide sequences is shown to be advantageous. A new variation of a method for constructing a minimal tree is presented. Our previous methods have involved first constructing a tree and then either proving that it is minimal or transforming it into a minimal tree. The approach presented in the present paper progressively builds up a tree, taxon by taxon. We illustrate this approach by using it to construct a minimal tree for ten mammalian haemoglobin alpha-chain sequences. Finally we define a measure of the complexity of the data and illustrate a method to derive a directed phylogenetic tree from the minimal tree.

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Molecular characterization of the coat protein gene revealed considerable diversity of viral species complex in Garlic (Allium sativum L.)

10.1101/2020.12.03.409680 ◽

2020 ◽

Author(s):

Abel Debebe Mitiku ◽

Dawit Tesfaye Degefu ◽

Adane Abraham ◽

Desta Mejan ◽

Pauline Asami ◽

...

Keyword(s):

Amino Acid ◽

Coat Protein ◽

Species Complex ◽

Sequence Data ◽

Amino Acid Sequences ◽

Viral Gene ◽

Planting Material ◽

Virus C ◽

Garlic Virus ◽

Material Exchange

AbstractGarlic is one of the most crucial Allium vegetables used as seasoning of foods. It has a lot of benefits from the medicinal and nutritional point of view; however, its production is highly constrained by both biotic and abiotic challenges. Among these, viral infections are the most prevalent factors affecting crop productivity around the globe. This experiment was conducted on eleven selected garlic accessions and three improved varieties collected from different garlic growing agro-climatic regions of Ethiopia. This study aimed to identify and characterize the isolated garlic virus using the coat protein (CP) gene and further determine their phylogenetic relatedness. RNA was extracted from fresh young leaves, thirteen days old seedlings, which showed yellowing, mosaic, and stunting symptoms. Pairwise molecular diversity for CP nucleotide and amino acid sequences were calculated using MEGA5. Maximum Likelihood tree of CP nucleotide sequence data of Allexivirus and Potyvirus were conducted using PhyML, while a neighbor-joining tree was constructed for the amino acid sequence data using MEGA5. From the result, five garlic viruses were identified viz. Garlic virus C (78.6 %), Garlic virus D (64.3 %), Garlic virus X (78.6 %), Onion yellow dwarf virus (OYDV) (100%), and Leek yellow stripe virus (LYSV) (78.6 %). The study revealed the presence of complex mixtures of viruses with 42.9 % of the samples had co-infected with a species complex of Garlic virus C, Garlic virus D, Garlic virus X, OYDV, and LYSV. Pairwise comparisons of the isolated Potyviruses and Allexiviruses species revealed high identity with that of the known members of their respected species. As an exception, less within species identity was observed among Garlic virus C isolates as compared with that of the known members of the species. Finally, our results highlighted the need for stepping up a working framework to establish virus-free garlic planting material exchange in the country which could result in the reduction of viral gene flow across the country.Author SummaryGarlic viruses are the most devastating disease since garlic is the most vulnerable crop due to their vegetative nature of propagation. Currently, the garlic viruses are the aforementioned production constraint in Ethiopia. However, so far very little is known on the identification, diversity, and dissemination of garlic infecting viruses in the country. Here we explore the prevalence, genetic diversity, and the presence of mixed infection of garlic viruses in Ethiopia using next generation sequencing platform. Analysis of nucleotide and amino acid sequences of coat protein genes from infected samples revealed the association of three species from Allexivirus and two species from Potyvirus in a complex mixture. Ultimately the article concludes there is high time to set up a working framework to establish garlic free planting material exchange platform which could result in a reduction of viral gene flow across the country.

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Molecular Cloning and Expression of Cu/Zn-Containing Superoxide Dismutase from Fasciola hepatica

Infection and Immunity ◽

10.1128/iai.68.7.3941-3948.2000 ◽

2000 ◽

Vol 68 (7) ◽

pp. 3941-3948 ◽

Cited By ~ 26

Author(s):

Tong-Soo Kim ◽

Younghun Jung ◽

Byoung-Kuk Na ◽

Ki-Sun Kim ◽

Pyung-Rim Chung

Keyword(s):

Superoxide Dismutase ◽

Amino Acid ◽

Fasciola Hepatica ◽

Human Subjects ◽

Amino Acid Sequences ◽

Cloning And Expression ◽

Gene Fragment ◽

Coding Region ◽

Sod Activity ◽

Degenerate Oligonucleotide

ABSTRACT The cytosolic superoxide dismutase (SOD) of Fasciola hepatica, a causative agent of fascioliasis, was purified and characterized. The enzyme consists of two identical subunits, each with an apparent molecular mass of 17.5 kDa. An analysis of the enzyme's primary structure and inhibition studies revealed that the enzyme is a copper/zinc-containing SOD (Cu/Zn-SOD). The enzyme activity was relatively stable in a broad pH range, from pH 7.0 to 10.0, and the enzyme showed maximum activity at pH 7.5. This enzyme also displayed strong antigenicity against sera of bovine and human subjects with fascioliasis. The SOD gene fragment was amplified by PCR with degenerate oligonucleotide primers derived from amino acid sequences conserved in the Cu/Zn-SODs of other organisms. An F. hepatica cDNA library was screened with the SOD gene fragment as a probe. As a result, a complete gene encoding the Cu/Zn-SOD was identified, and its nucleotide sequence was determined. The gene had an open reading frame of 438 bp and 146 deduced amino acids. Comparison of the deduced amino acid sequence of the enzyme with previously reported Cu/Zn-SOD amino acid sequences revealed considerably high homologies. The coding region of the F. hepatica Cu/Zn-SOD was cloned and expressed in Escherichia coli. Staining of native polyacrylamide gel for SOD activity of the expressed protein revealed SOD activity that was inactivated by potassium cyanide and hydrogen peroxide but not by sodium azide. This means that the presence of the recombinant fusion protein is indicative of Cu/Zn-SOD. The expressed protein also reacted with sera of bovine and human subjects with fascioliasis, but it did not react with sera of uninfected bovine and human subjects.

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Nucleotide and derived amino acid sequences of a cDNA coding for pre-uteroglobin from the lung of the hare (Lepus capensis)

Biochemical Journal ◽

10.1042/bj2350895 ◽

1986 ◽

Vol 235 (3) ◽

pp. 895-898 ◽

Cited By ~ 12

Author(s):

M S López de Haro ◽

A Nieto

Keyword(s):

Amino Acids ◽

Amino Acid ◽

Nucleotide Sequence ◽

Amino Acid Sequence ◽

Amino Acid Sequences ◽

Untranslated Regions ◽

Coding Region ◽

Homologous Proteins ◽

Lepus Capensis ◽

Rabbit Gene

An almost full-length cDNA coding for pre-uteroglobin from hare lung was cloned and sequenced. The derived amino acid sequence indicated that hare pre-uteroglobin contained 91 amino acids, including a signal peptide of 21 residues. Comparison of the nucleotide sequence of hare pre-uteroglobin cDNA with that previously reported for the rabbit gene indicated five silent point substitutions and six others leading to amino acid changes in the coding region. The untranslated regions of both pre-uteroglobin mRNAs were very similar. The amino acid changes observed are discussed in relation to the different progesterone-binding abilities of both homologous proteins.

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Alignment of Amino Acid and DNA Sequences of Human Proline-rich Proteins

Critical Reviews in Oral Biology & Medicine ◽

10.1177/10454411930040030501 ◽

1993 ◽

Vol 4 (3) ◽

pp. 287-292 ◽

Cited By ~ 12

Author(s):

D.L. Kauffman ◽

P.J. Keller ◽

A. Bennick ◽

M. Blum

Keyword(s):

Amino Acid ◽

Dna Sequences ◽

Sequence Data ◽

Gel Filtration ◽

Exchange Chromatography ◽

Amino Acid Sequences ◽

Secreted Proteins ◽

Dna Encoding ◽

Protein Amino Acid ◽

Primary Gene

Human proline-rich proteins (PRPs) constitute a complex family of salivary proteins that are encoded by a small number of genes. The primary gene product is cleaved by proteases, thereby giving rise to about 20 secreted proteins. To determine the genes for the secreted PRPs, therefore, it is necessary to obtain sequences of both the secreted proteins and the DNA encoding these proteins. We have sequenced most PRPs from one donor (D.K.) and aligned the protein sequences with available DNA sequences from unrelated individuals. Partial sequence data have now been obtained for an additional PRP from D.K. named II-1. This protein was purified from parotid saliva by gel filtration and ion-exchange chromatography. Peptides were obtained by cleavage with trypsin, clostripain, and N-bromosuccinimide, followed by column chromatography. The peptides were sequenced on a gas-phase protein sequenator. Overlapping peptide sequences were obtained for most of II-1 and aligned with translated DNA sequences. The best fit was obtained with clones containing sequences for the allele PRB4" (Lyons et al., 1988). However, there was not complete identity of the protein amino acid sequence and the DNA-derived sequences, indicating that II-1 is not encoded by PRB4". Other PRPs isolated from D.K. also fail to conform to any DNA structure so far reported. This shows the need to obtain amino acid sequences and corresponding DNA sequences from the same person to assign genes for the PRPs and to determine the location of the postribosomal cleavage points in the primary translation product.

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No polymorphisms in the coding region of the prion-like protein gene in Thoroughbred racehorses

Acta Veterinaria Hungarica ◽

10.1556/004.2019.019 ◽

2019 ◽

Vol 67 (2) ◽

pp. 174-182 ◽

Cited By ~ 4

Author(s):

Min-Ju Jeong ◽

Byung-Hoon Jeong

Keyword(s):

Amino Acid ◽

Prion Protein ◽

Protein Gene ◽

Prion Diseases ◽

Amino Acid Sequences ◽

Prion Protein Gene ◽

Coding Region ◽

Thoroughbred Racehorses ◽

Thoroughbred Horses ◽

Protein Isoform

Prion diseases are fatal neurodegenerative diseases characterised by the accumulation of an abnormal prion protein isoform (PrPSc), which is converted from the normal prion protein (PrPC). Prion diseases have been reported in an extensive number of species but not in horses up to now; therefore, horses are known to be a species resistant to prion diseases. The prion-like protein gene (PRND) is closely located downstream of the prion protein gene (PRNP) and the prion-like protein (Doppel) is a homologue with PrP. Previous studies have shown that an association between prion diseases and polymorphisms of the PRND gene is reported in the main hosts of prion diseases. Hence, we examined the genetic variations of the PRND gene in Thoroughbred horses. Interestingly, polymorphisms of the PRND gene were not detected. In addition, we conducted a comparative analysis of the amino acid sequences of the PRND gene to identify the differences between horses and other species. The amino acid sequence of the horse PRND gene showed the highest identity to that of sheep (83.7%), followed by that of goats, cattle and humans. To the best of our knowledge, this is the first genetic study of the PRND gene in horses.

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Molecular cloning and evolutionary analysis of the GJA1 (connexin43) gene from bats (Chiroptera)

Genetics Research ◽

10.1017/s0016672309000032 ◽

2009 ◽

Vol 91 (2) ◽

pp. 101-109 ◽

Cited By ~ 1

Author(s):

LI WANG ◽

GANG LI ◽

JINHONG WANG ◽

SHAOHUI YE ◽

GARETH JONES ◽

...

Keyword(s):

Amino Acid ◽

Phylogenetic Reconstruction ◽

Purifying Selection ◽

Likelihood Method ◽

Evolutionary Analysis ◽

Coding Region ◽

Specific Amino Acid ◽

Junction Protein ◽

Gap Junction Protein ◽

Species Specific

SummaryGap junction protein connexin43 (Cx43), encoded by the GJA1 gene, is the most abundant connexin in the cardiovascular system and was reported as a crucial factor maintaining cardiac electrical conduction, as well as having a very important function in facilitating the recycling of potassium ions from hair cells in the cochlea back into the cochlear endolymph during auditory transduction processes. In mammals, bats are the only taxon possessing powered flight, placing exceptional demand on many organismal processes. To meet the demands of flying, the hearts of bats show many specialties. Moreover, ultrasonic echolocation allows bat species to orientate and often detect and locate food in darkness. In this study, we cloned the full-length coding region of GJA1 gene from 12 different species of bats and obtained orthologous sequences from other mammals. We used the maximum likelihood method to analyse the evolution of GJA1 gene in mammals and the lineage of bats. Our results showed this gene is much conserved in mammals, as well as in bats' lineage. Compared with other mammals, we found one private amino acid substitution shared by bats, which is located on the inner loop domain, as well as some species-specific amino acid substitutions. The evolution rate analyses showed the signature of purifying selection on not only different classification level lineages but also the different domains and amino acid residue sites of this gene. Also, we suggested that GJA1 gene could be used as a good molecular marker to do the phylogenetic reconstruction.

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The cDNA and protein sequences of human lactate dehydrogenase B

Biochemical Journal ◽

10.1042/bj2480933 ◽

1987 ◽

Vol 248 (3) ◽

pp. 933-936 ◽

Cited By ~ 31

Author(s):

I Sakai ◽

F S Sharief ◽

Y C Pan ◽

S S Li

Keyword(s):

Amino Acid ◽

Lactate Dehydrogenase ◽

Amino Acid Composition ◽

Acid Composition ◽

Amino Acid Sequences ◽

British Library ◽

Amino Acid Residues ◽

Coding Region ◽

Cdna Insert ◽

Protein Coding

Human lactate dehydrogenase B (LDH-B) cDNA was isolated and sequenced. The LDH-B cDNA insert consists of the protein-coding sequence (999 bp), the 5′ (54 bp) and 3′ (203 bp) non-coding regions, and the poly(A) tail (50 bp). The predicted sequence of 333 amino acid residues was confirmed by amino acid composition and/or sequence analyses of a total of 185 (56%) residues from tryptic peptides of human LDH-B protein. The nucleotide and amino acid sequences of the human LDH-B coding region show 68% and 75% homologies respectively with those of the human LDH-A. The peptide map and amino acid composition data have been deposited as Supplementary Publication SUP 50139 (7 pages) at the British Library Lending Division, Boston Spa, Wetherby, West Yorkshire LS23 7BQ, U.K., from whom copies are available on prepayment [see Biochem. J. (1987) 241, 5].

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Isolation and characterization of the pea cytochrome c oxidase Vb gene

Genome ◽

10.1139/g06-105 ◽

2006 ◽

Vol 49 (11) ◽

pp. 1481-1489 ◽

Cited By ~ 1

Author(s):

Nakao Kubo ◽

Shin-ichi Arimura ◽

Nobuhiro Tsutsumi ◽

Koh-ichi Kadowaki ◽

Masashi Hirai

Keyword(s):

Amino Acid ◽

Cytochrome C ◽

Cytochrome C Oxidase ◽

Fluorescent Proteins ◽

Amino Acid Sequences ◽

Homology Search ◽

Coding Region ◽

Angiosperm Evolution ◽

Isolation And Characterization ◽

Duplication Events

Three copies of the gene that encodes cytochrome c oxidase subunit Vb were isolated from the pea (PscoxVb-1, PscoxVb-2, and PscoxVb-3). Northern Blot and reverse transcriptase-PCR analyses suggest that all 3 genes are transcribed in the pea. Each pea coxVb gene has an N-terminal extended sequence that can encode a mitochondrial targeting signal, called a presequence. The localization of green fluorescent proteins fused with the presequence strongly suggests the targeting of pea COXVb proteins to mitochondria. Each pea coxVb gene has 5 intron sites within the coding region. These are similar to Arabidopsis and rice, although the intron lengths vary greatly. A phylogenetic analysis of coxVb suggests the occurrence of gene duplication events during angiosperm evolution. In particular, 2 duplication events might have occurred in legumes, grasses, and Solanaceae. A comparison of amino acid sequences in COXVb or its counterpart shows the conservation of several amino acids within a zinc finger motif. Interestingly, a homology search analysis showed that bacterial protein COG4391 and a mitochondrial complex I 13 kDa subunit also have similar amino acid compositions around this motif. Such similarity might reflect evolutionary relationships among the 3 proteins.

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