A comparative study of repeated sequences in the SM50 gene of some sea urchins

Spicule matrix proteins of sea urchin embryo are the specific products of the micromere / primary mesenchyme cell (PMC) lineage, and are considered to be involved in spicule formation (Wilt, 1999). One of these proteins, SM50, has been described for three species: Strongylocentrotus purpuratus (SP), Lytechinus pictus (Lp) and Hemicentrotus pulcherrimus (Hp) (for references see Wilt, 1999). The nucleotide and amino acid sequences are well conserved in these species. SM50 proteins of these species have repetitive amino acid sequences in the carboxyl-terminal half of the proteins. Therefore, examination of SM50 sequences, especially the repetitive sequence region, in various species will help an understanding of the process of sea urchin ontogeny and evolution. In this study we tried to amplify, by PCR, the SM50 sequences of species for which no sequence data are reported.Total DNA was extracted from the sperm of sea urchins by standard procedures. The purified DNA was subjected to PCR to amplify the repetitive amino acid region and its upstream region. The primers were designed based on the highly conserved sequences in the reported SM50 as Consensus-Degenerate Hybrid Oligonucleotide Primers (Rose et al., 1997). The amplified products were gel-purified, and sequenced using ABI PRISM 310 Genetic Analyzer using PCR primers. The determined nucleotide sequences were translated into amino acid sequences and compared among species with a phylogenetic tree constructed by the neighbour-joining method. For indirect immunofluorescent staining, embryos were fixed with 70% methanol and reacted with rabbit antiserum against recombinant SM50 protein.

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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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Identification of mariner-like elements in Sitodiplosis mosellana (Diptera: Cecidomyiidae)

The Canadian Entomologist ◽

10.4039/n05-007 ◽

2006 ◽

Vol 138 (2) ◽

pp. 138-146 ◽

Cited By ~ 4

Author(s):

O. Mittapalli ◽

R.H. Shukle ◽

I.L. Wise

Keyword(s):

Phylogenetic Analysis ◽

Amino Acid ◽

Blot Analysis ◽

Copy Number ◽

Southern Blot Analysis ◽

Pcr Primers ◽

Amino Acid Sequences ◽

Degenerate Pcr ◽

Sitodiplosis Mosellana ◽

Wheat Midge

AbstractMariner-like element sequences were recovered from the genome of the orange wheat midge, Sitodiplosis mosellana (Géhin), with degenerate PCR primers designed to conserved regions of mariner transposases. The deduced amino acid sequences of the mariner-like transposases from S. mosellana showed 67% to 78% identity with the peptide sequences of other mariner transposases. A phylogenetic analysis revealed that the mariner-like elements from S. mosellana grouped in the mauritiana subfamily of mariner transposons. Results from Southern blot analysis suggest mariner-like elements are at a moderate copy number in the genome of S. mosellana.

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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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Sulphoacetaldehyde sulpho-lyase (EC 4.4.1.12) from Desulfonispora thiosulfatigenes: purification, properties and primary sequence

Biochemical Journal ◽

10.1042/bj3570581 ◽

2001 ◽

Vol 357 (2) ◽

pp. 581-586 ◽

Cited By ~ 20

Author(s):

Karin DENGER ◽

Jürgen RUFF ◽

Ulrike REIN ◽

Alasdair M. COOK

Keyword(s):

Amino Acid ◽

Molecular Mass ◽

Pcr Primers ◽

Amino Acid Sequences ◽

Thiamine Pyrophosphate ◽

Strictly Anaerobic ◽

Laser Desorption Ionization ◽

Native Form ◽

Ionization Time ◽

Sds Page

The strictly anaerobic bacterium Desulfonispora thiosulfatigenes ferments taurine via sulphoacetaldehyde, which is hydrolysed to acetate and sulphite by sulphoacetaldehyde sulpho-lyase (EC 4.4.1.12). The lyase was expressed at high levels and a two-step, 4.5-fold purification yielded an apparently homogeneous soluble protein, which was presumably a homodimer in its native form; the molecular mass of the subunit was about 61kDa (by SDS/PAGE). The mass was determined to be 63.8kDa by matrix-assisted laser-desorption ionization–time-of-flight (MALDI–TOF) MS. The purified enzyme converted 1mol of sulphoacetaldehyde to 1mol each of sulphite and acetate, but no requirement for thiamine pyrophosphate (TPP) was detected. The N-terminal and two internal amino acid sequences were determined, which allowed us to generate PCR primers. The gene was amplified and sequenced. The DNA sequence had no significant homologue in the databases searched, whereas the derived amino acid sequence indicated an oxo-acid lyase, revealed a TPP-binding site and gave a derived molecular mass of 63.8kDa.

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Phenotypic and Enzymatic Comparative Analysis of the Novel KPC Variant KPC-5 and Its Evolutionary Variants, KPC-2 and KPC-4

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00734-08 ◽

2008 ◽

Vol 53 (2) ◽

pp. 557-562 ◽

Cited By ~ 67

Author(s):

Daniel J. Wolter ◽

Philip M. Kurpiel ◽

Neil Woodford ◽

Marie-France I. Palepou ◽

Richard V. Goering ◽

...

Keyword(s):

Amino Acid ◽

Amino Acid Sequences ◽

Single Amino Acid ◽

Upstream Region ◽

The Novel ◽

Carbapenem Resistant ◽

Flanking Regions ◽

Hydrolysis Of ◽

Additional Amino Acid

ABSTRACT A novel Klebsiella pneumoniae carbapenemase (KPC) variant, designated bla KPC-5, was discovered in a carbapenem-resistant Pseudomonas aeruginosa clinical isolate from Puerto Rico. Characterization of the upstream region of bla KPC-5 showed significant differences from the flanking regions of other bla KPC variants. Comparison of amino acid sequences with those of other KPC enzymes revealed that KPC-5 was an intermediate between KPC-2 and KPC-4, differing from KPC-2 by a single amino acid substitution (Pro103→Arg), while KPC-4 contained Pro103→Arg plus an additional amino acid change (Val239→Gly). Transformation studies with an Escherichia coli recipient strain showed differences in the properties of the KPC variants. KPC-4 and KPC-5 both had pIs of 7.65, in contrast with the pI of 6.7 for KPC-2. KPC-2 transformants were less susceptible to the carbapenems than KPC-4 and KPC-5 transformants. These data correlated with higher rates of imipenem hydrolysis for KPC-2 than for KPC-4 and KPC-5. However, KPC-4 and KPC-5 transformants had higher ceftazidime MICs, and the enzymes from these transformants had slightly better hydrolysis of this drug than KPC-2. KPC-4 and KPC-5 were more sensitive than KPC-2 to inhibition by clavulanic acid in both susceptibility testing and hydrolysis assays. Thus, KPC enzymes may be evolving through stepwise mutations to alter their spectra of activity.

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Phylogeny and expression of axonemal and cytoplasmic dynein genes in sea urchins.

Molecular Biology of the Cell ◽

10.1091/mbc.5.1.57 ◽

1994 ◽

Vol 5 (1) ◽

pp. 57-70 ◽

Cited By ~ 121

Author(s):

B H Gibbons ◽

D J Asai ◽

W J Tang ◽

T S Hays ◽

I R Gibbons

Keyword(s):

Sea Urchin ◽

Heavy Chain ◽

Sea Urchins ◽

Early Stage ◽

Single Gene ◽

Cytoplasmic Dynein ◽

Phosphate Binding ◽

Atp Binding Site ◽

Heavy Chains ◽

Amino Acid Region

Transcripts approximately 14.5 kilobases in length from 14 different genes that encode for dynein heavy chains have been identified in poly(A)+ RNA from sea urchin embryos. Analysis of the changes in level of these dynein transcripts in response to deciliation, together with their sequence relatedness, suggests that 11 or more of these genes encode dynein isoforms that participate in regeneration of external cilia on the embryo, whereas the single gene whose deduced sequence closely resembles that of cytoplasmic dynein in other organisms appears not to be involved in this regeneration. The four consensus motifs for phosphate binding found previously in the beta heavy chain of sea urchin dynein are present in all five additional isoforms for which extended sequences have been obtained, suggesting that these sites play a significant role in dynein function. Sequence analysis of a approximately 400 amino acid region encompassing the putative hydrolytic ATP-binding site shows that the dynein genes fall into at least six distinct classes. Most of these classes in sea urchin have a high degree of sequence identity with one of the dynein heavy chain genes identified in Drosophila, indicating that the radiation of the dynein gene family into the present classes occurred at an early stage in the evolution of eukaryotes. Evolutionary changes in cytoplasmic dynein have been more constrained than those in the axonemal dyneins.

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ESTIMATION OF TIME OF DIVERGENCE FROM PHYLOGENETIC STUDIES

Canadian Journal of Genetics and Cytology ◽

10.1139/g77-024 ◽

1977 ◽

Vol 19 (2) ◽

pp. 217-223 ◽

Cited By ~ 35

Author(s):

Ranajit Chakraborty

Keyword(s):

Amino Acid ◽

Sequence Data ◽

Amino Acid Sequences ◽

Evolutionary Significance ◽

Simultaneous Estimation ◽

Homologous Proteins ◽

Phylogenetic Structure ◽

Phylogenetic Studies ◽

Base Sequences ◽

Time Of Divergence

Recent studies with comparative data on base sequences of homologous DNAs or amino acid sequences of homologous proteins indicate that simultaneous estimation of phylogenetic structure and time of divergence is often cumbersome and time consuming. On the other hand, when the topology of an evolutionary tree is known, it is shown in this paper that the least squares theory may be applied to obtain simple estimates of the relative time lengths for each segment of the tree under the assumption of uniform random substitutions in each segment. The method is illustrated with amino acid sequence data on various globin molecules and cytochrome c. The evolutionary significance of some of the estimates is also discussed.

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RHIVDB: A Freely Accessible Database of HIV Amino Acid Sequences and Clinical Data of Infected Patients

Frontiers in Genetics ◽

10.3389/fgene.2021.679029 ◽

2021 ◽

Vol 12 ◽

Author(s):

Olga Tarasova ◽

Anastasia Rudik ◽

Dmitry Kireev ◽

Vladimir Poroikov

Keyword(s):

Amino Acid ◽

Sequence Data ◽

Drug Combinations ◽

Biological Data ◽

Amino Acid Sequences ◽

Web Database ◽

Cd4 Cell Count ◽

Viral Load Data ◽

Treatment Data ◽

Cd4 Cell

Human immunodeficiency virus (HIV) infection remains one of the most severe problems for humanity, particularly due to the development of HIV resistance. To evaluate an association between viral sequence data and drug combinations and to estimate an effect of a particular drug combination on the treatment results, collection of the most representative drug combinations used to cure HIV and the biological data on amino acid sequences of HIV proteins is essential. We have created a new, freely available web database containing 1,651 amino acid sequences of HIV structural proteins [reverse transcriptase (RT), protease (PR), integrase (IN), and envelope protein (ENV)], treatment history information, and CD4+ cell count and viral load data available by the user’s query. Additionally, the biological data on new HIV sequences and treatment data can be stored in the database by any user followed by an expert’s verification. The database is available on the web at http://www.way2drug.com/rhivdb.

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Phylogenetic relationships of the nematode subfamily Phascolostrongylinae from macropodid and vombatid marsupials inferred using mitochondrial protein sequence data

Parasites & Vectors ◽

10.1186/s13071-021-05028-2 ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

Tanapan Sukee ◽

Ian Beveridge ◽

Anson V. Koehler ◽

Ross Hall ◽

Robin B. Gasser ◽

...

Keyword(s):

Amino Acid ◽

Phylogenetic Relationships ◽

Sequence Data ◽

Mitochondrial Protein ◽

Amino Acid Sequences ◽

Internal Transcribed Spacers ◽

Nuclear Ribosomal Dna ◽

Phylogenetic Position ◽

Data Sets ◽

Sister Relationship

Abstract Background The subfamily Phascolostrongylinae (Superfamily Strongyloidea) comprises nematodes that are parasitic in the gastrointestinal tracts of macropodid (Family Macropodidae) and vombatid (Family Vombatidae) marsupials. Currently, nine genera and 20 species have been attributed to the subfamily Phascolostrongylinae. Previous studies using sequence data sets for the internal transcribed spacers (ITS) of nuclear ribosomal DNA showed conflicting topologies between the Phascolostrongylinae and related subfamilies. Therefore, the aim of this study was to validate the phylogenetic relationships within the Phascolostrongylinae and its relationship with the families Chabertiidae and Strongylidae using mitochondrial amino acid sequences. Methods The sequences of all 12 mitochondrial protein-coding genes were obtained by next-generation sequencing of individual adult nematodes (n = 8) representing members of the Phascolostrongylinae. These sequences were conceptually translated and the phylogenetic relationships within the Phascolostrongylinae and its relationship with the families Chabertiidae and Strongylidae were inferred from aligned, concatenated amino acid sequence data sets. Results Within the Phascolostrongylinae, the wombat-specific genera grouped separately from the genera occurring in macropods. Two of the phascolostrongyline tribes were monophyletic, including Phascolostrongylinea and Hypodontinea, whereas the tribe Macropostrongyloidinea was paraphyletic. The tribe Phascolostrongylinea occurring in wombats was closely related to Oesophagostomum spp., also from the family Chabertiidae, which formed a sister relationship with the Phascolostrongylinae. Conclusion The current phylogenetic relationship within the subfamily Phascolostrongylinae supports findings from a previous study based on ITS sequence data. This study contributes also to the understanding of the phylogenetic position of the subfamily Phascolostrongylinae within the Chabertiidae. Future studies investigating the relationships between the Phascolostrongylinae and Cloacininae from macropodid marsupials may advance our knowledge of the phylogeny of strongyloid nematodes in marsupials. Graphical Abstract

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