scholarly journals In silico characterization and expression profiles of zinc transporter-like (LOC100037509) gene of tomato

2020 ◽  
Author(s):  
Ahmad Humayan Kabir
Keyword(s):  
Transcriptional Start Site ◽  
Phosphorylation Site ◽  
Alpha Helix ◽  
Glycosylation Site ◽  
Zinc Transporter ◽  
Solanum Pennellii ◽  
Phylogenetic Studies ◽  
Zn Homeostasis ◽  
Relationship Of ◽  
Unique Signal

ABSTRACTZinc (Zn) is an essential microelement for plants. ZIP transporters play a critical role in Zn homeostasis in plants. This in silico study characterizes different characteristics of putative Zn transporter of tomato (Solyc07g065380) and its homologs. A total of 10 ZIP protein homologs were identified across nine plant species by protein BLAST. All these ZIP protein homologs located at chromosome 7 showed 305-350 amino acid residues, 7-8 transmembrane helices, and stable instability index. Further, these ZIP protein homologs are localized in the plasma membrane at the subcellular level corresponding to the ZIP zinc transporter (PF02535) domain. Gene organization analysis reveals the presence of 3 exon along with the position of the promoter, TATA-box, transcriptional start site, and splice sites in these ZIP transporter homologs, in which tomato ZIP transporter (NM_001247420.1) contains a promoter, TATA-box, transcriptional start site at 500, 911 and 946 bp, respectively along with several splice sites, which may be useful for targeting binding sites and transcription factor analysis. Further, the cutting sites and restriction enzymes of each ZIP gene homologs might be helpful for future transgenic studies underlying Zn homeostasis. MEMO displayed five conserved motifs associated with the ZIP zinc transporter, N-glycosylation site, and phosphorylation site. Phylogenetic studies reveal a closet relationship of Solyc07g065380 with Solanum pennellii homolog, while ZIP transporter of Nicotiana sylvestris and Nicotiana tabacum predicted to be in close connection. The Solyc07g065380 transporter is predominantly linked to several uncharacterized zinc metal ion transporters and expressed in diverse anatomical part, developmental stage, and subjected to pathogen and heat stress. The secondary structural prediction reveals unique signal peptide in the ZIP protein homologs of S. lycopersicum and S. pennellii along with extended alpha-helix. These bioinformatics analyses might provide essential background to perform wet-lab experiments and to understand Zn homeostasis for the development of Zn-biofortified crops.Key message♦ ZIP protein homologs are localized in the plasma membrane and are linked to ZIP zinc transporter (PF02535) domain at chromosome 7.♦ ZIP protein motifs are associated with the ZIP zinc transporter, N-glycosylation site, and phosphorylation site.♦ Phylogenetic studies reveal a closet relationship of Solyc07g065380 with Solanum pennellii homolog.♦ ZIP protein homologs of S. lycopersicum and S. pennellii show unique signal peptide along with extended alpha-helix.

Phylogeny of Echiura updated, with a revised taxonomy to reflect their placement in Annelida as sister group to Capitellidae

2020 ◽  
Vol 34 (1) ◽  
pp. 101 ◽  
Author(s):  
Ryutaro Goto ◽  
James Monnington ◽  
Marija Sciberras ◽  
Isao Hirabayashi ◽  
Greg W. Rouse
Keyword(s):  
Molecular Phylogeny ◽  
Deep Sea ◽  
Sister Group ◽  
Molecular Data ◽  
Monterey Bay ◽  
Phylogenetic Studies ◽  
Littoral Zones ◽  
Family Level ◽  
Relationship Of ◽  
The Relationship

Echiura (commonly called spoon worms) are derived annelids that have an unsegmented sausage-shaped body with a highly extensible anterior end (i.e. a proboscis). Echiura currently contains two superfamilies: Echiurioidea (with Echiuridae, Urechidae and Thalassematidae) and Bonellioidea (with Bonelliidae, and Ikedidae). Ikedidae contains only Ikeda, which is distinctive in having a huge trunk, a highly elongate proboscis with stripes or dots, and numerous gonoducts. A recent molecular phylogeny of Echiura recovered Ikedidae as the sister group to Bonelliidae. However, due to relatively low support values for the monophyly of Bonelliidae, this relationship remains problematic. In this study, we reinvestigated the relationship of Bonelliidae and Ikedidae using an expanded dataset with more taxa and genes. In contrast to the previous results, our analyses strongly support that Ikeda is nested within Bonelliidae due to the placement of Maxmuelleria. On the basis of this result, we synonymise Ikedidae with Bonelliidae and transfer Ikeda to the latter, the diagnosis of which is amended. In addition, we synonymise Urechidae with its sister group Echiuridae because they share the synapomorphy of having anal chaetae rings. Furthermore, considering that recent phylogenetic studies have consistently recovered Echiura as the sister group to Capitelliidae within Annelida, we drop the rank of the echiuran clade to family-level and propose a revised classification: Thalassematidae with two subfamilies, Thalassematinae (with two tribes Echiurini and Thalassematini) and Bonelliinae. In addition, we identified a sample collected from the deep sea (~1820 m) of Monterey Bay, California, based on its molecular data. This terminal unexpectedly formed the sister group to the eight genera of Thalassematini, most members of which are inhabitants of littoral zones.

Phylogenetic studies on uncultured Frankia populations in nodules of Datisca cannabina

1994 ◽  
Vol 40 (4) ◽  
pp. 313-318 ◽  
Author(s):  
M. Sajjad Mirza ◽  
Dittmar Hahn ◽  
Svetlana V. Dobritsa ◽  
Antoon D. L. Akkermans
Keyword(s):  
16S Rrna ◽  
Root Nodules ◽  
Alnus Glutinosa ◽  
Rrna Gene ◽  
16S Rrna Sequence ◽  
Phylogenetic Studies ◽  
Close Relationship ◽  
16S Rrna Sequence Analysis ◽  
Relationship Of ◽  
The 16S Rrna Gene

Part of the 16S rRNA gene was amplified directly from uncultured endophyte populations within the root nodules of Datisca cannabina and three strains isolated from nodules of Alnus glutinosa (AgKG′84/4), Coriaria nepalensis (Cn3), and D. cannabina (Dc2). Sequence comparison based on 930 nucleotides indicated that the endophyte of D. cannabina nodules belongs to the genus Frankia and is highly related to the endophyte of C. nepalensis root nodules. The relatedness of the endophytes of C. nepalensis and D. cannabina nodules was also reflected by closely related nifH sequences amplified from the nodules. 16S rRNA sequence analysis of the noninfective strains obtained from both D. cannabina (Dc2) and C. nepalensis (Cn3) nodules also revealed the close relationship of these strains to the genus Frankia.Key words: nitrogen fixation, Frankia, 16S rRNA, nifH.

scholarly journals Visualizing key hinges and a potential major source of compliance in the lever arm of myosin

2010 ◽  
Vol 108 (1) ◽  
pp. 114-119 ◽  
Author(s):  
Jerry H. Brown ◽  
V. S. Senthil Kumar ◽  
Elizabeth O’Neall-Hennessey ◽  
Ludmila Reshetnikova ◽  
Howard Robinson ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Heavy Chain ◽  
Light Chain ◽  
Potential Role ◽  
Phosphorylation Site ◽  
Alpha Helix ◽  
Localized Source ◽  
Lever Arm ◽  
Sea Scallop ◽  
Relative Proximity

We have determined the 2.3-Å-resolution crystal structure of a myosin light chain domain, corresponding to one type found in sea scallop catch (“smooth”) muscle. This structure reveals hinges that may function in the “on” and “off” states of myosin. The molecule adopts two different conformations about the heavy chain “hook” and regulatory light chain (RLC) helix D. This conformational change results in extended and compressed forms of the lever arm whose lengths differ by 10 Å. The heavy chain hook and RLC helix D hinges could thus serve as a potential major and localized source of cross-bridge compliance during the contractile cycle. In addition, in one of the molecules of the crystal, part of the RLC N-terminal extension is seen in atomic detail and forms a one-turn alpha-helix that interacts with RLC helix D. This extension, whose sequence is highly variable in different myosins, may thus modulate the flexibility of the lever arm. Moreover, the relative proximity of the phosphorylation site to the helix D hinge suggests a potential role for conformational changes about this hinge in the transition between the on and off states of regulated myosins.

scholarly journals Bioinformatic characterization of the Transmembrane protein95 gene (TMEM95) in Murrah buffalo (Bubalus bubalis)

2021 ◽  
Vol 91 (1) ◽  
pp. 11-18
Author(s):  
Sampathirao Shireesha ◽  
◽  
Krovvidi Sudhakar ◽  
Regula Vinoo ◽  
Chappidi V. Seshaiah ◽  
...  
Keyword(s):  
Protein Function ◽  
Male Fertility ◽  
Leucine Zipper ◽  
Phosphorylation Site ◽  
Glycosylation Site ◽  
Sequence Information ◽  
Missense Mutations ◽  
Murrah Buffalo ◽  
Synonymous Mutations ◽  
Male Subfertility

Idiopathic male subfertility is often a neglected phenotype with respect to male fertility in bovines. The gene TMEM95 plays a crucial role in idiopathic male subfertility in cattle. Using the DNA sequence information from cattle TMEM95 gene, we characterized the gene in Murrah buffalo. A total of 2.6 kb of a fragment orthologous to cattle was sequenced from Murrah buffalo and Gir cattle. A 2 bp deletion is present in Murrah buffalo, causing missense mutations in three isoforms that are present in cattle. The functional effects of various non-synonymous mutations were predicted using the SNAP2 program, and showed that the non-synonymous SNPs could affect the protein function. Functional motif annotation revealed the presence of a Casein kinase II phosphorylation site that plays an important role in sperm morphology, Leucine zipper pattern, N-myristoylation site, protein kinase C phosphorylation site, CHRD domain profile, N-glycosylation site and HIT zinc finger motifs in cattle. The HIT ZF motif is absent in all of the functional isoforms in buffalo. The results together suggest that the subfertility gene TMEM95 in cattle and buffalo must have evolved with different functions but plays a role in male fertility as in other mammals.

scholarly journals A new species of Knodus (Characiformes: Characidae: Stevardiinae) from the rio Aripuanã, rio Madeira basin, Brazil

2020 ◽  
Vol 18 (2) ◽  
Author(s):  
Naércio A. Menezes ◽  
Katiane M. Ferreira ◽  
André L. Netto-Ferreira
Keyword(s):  
New Species ◽  
Lateral Line ◽  
Body Depth ◽  
Posterior Teeth ◽  
Incertae Sedis ◽  
Phylogenetic Studies ◽  
Relationship Of ◽  
A New Species ◽  
Rio Madeira ◽  
Pelvic Fin

ABSTRACT A new species of the characid genus Knodus is described from the rio Aripuanã (rio Madeira basin). It can be distinguished from its congeners by its very low body depth, the presence of tri- to pentacuspid teeth on the outer premaxillary series, with the median cuspid larger than the lateral ones, the teeth of the inner premaxillary series pentacuspid, distinctly larger than those of the outer series, the maxillary teeth tri- to pentacuspid, with the median cusp slightly larger than the lateral ones, the four anteriormost dentary teeth pentacuspid, the smaller posterior teeth tri- to pentacuspid, a complete lateral line with 36-38 scales, 3 longitudinal scale series from pelvic fin origin to lateral line, and 11-12 circumpeduncular scales. The new species is also compared to incertae sedis species of ‘Bryconamericus’ from northern South America since phylogenetic studies suggest a closer relationship of those species with Knodus.

HUNTINGTON GENE ONTOLOGICAL STUDY AND ORTHOLOGICAL ANALYSIS

2016 ◽  
Vol 1 (2) ◽  
pp. 65
Author(s):  
Muhammad Ilyas ◽  
Asif Mir ◽  
Sobiah Rauf ◽  
Sidrah Nazir ◽  
Humera Javed
Keyword(s):  
Neurodegenerative Disorder ◽  
Evolutionary Relationship ◽  
Causative Gene ◽  
Syntenic Relationship ◽  
Complete Penetrance ◽  
Phylogenetic Studies ◽  
Abnormal Movements ◽  
Psychiatric Disturbances ◽  
Relationship Of ◽  
Insight Into

Huntington gene is located on chromosome 4p16.3 IT15 locus considered a major causative gene of Huntington disorder. HTT is a neurodegenerative disorder mutation in gene cause abnormal movements and psychiatric disturbances. HTT is inherited in an autosomal dominant manner with almost complete penetrance and till now, no research studies provide insight into HTT gene. Bioinformatics analysis includes transcription factors binding sites, phylogenetic studies with reference to various selected orthologs and syntenic relationship of HTT gene. Our study showed that in HTT gene majority of the portion is conserved among two orthologs chimpanzee and mouse in significance to human. These studies also revealed information about conservation of genes among different ortholog species and their evolutionary relationship.

Effects of N224 glycosylation in Saccharomycopsis fibuligera R64 α-amylase on enzyme activity and stability

2021 ◽  
Vol 17 ◽  
Author(s):  
Yovin Sugijo ◽  
Tina Dewi Rosahdi ◽  
Fernita Puspasari ◽  
Wangsa Tirta Ismaya ◽  
Khomaini Hasan ◽  
...  
Keyword(s):  
Thermal Stability ◽  
Enzyme Activity ◽  
Evolutionary Relationship ◽  
Glycosylation Site ◽  
Site Directed Mutagenesis ◽  
Wild Type ◽  
Saccharomycopsis Fibuligera ◽  
Glycosylation Sites ◽  
Starch Substrate ◽  
Relationship Of

Background: The amino acid sequence of an α-amylase of the yeast Saccharomycopsis fibuligera R64 (SfamyR64) contains the two putative N-linked glycosylation sites N153 and N224. N224 is hypothetically responsible for the binding of starch substrate because it is highly conserved among SfamyR64 homologs. Objective: To test whether N224 plays a key role in enzyme activity and stability. Methods: N224Q substitution was introduced by site-directed mutagenesis. The wild type and the mutant were independently over-produced in Pichia pastoris KM71. Activity of the wild type and of the mutant were compared, and their thermal-stability was assessed using heat treatments. The evolutionary relationship of SfamyR64 with its structural homologs with different glycosylation patterns was examined. Results: Activity of the N224Q mutant was approximately 80% lower than that of the wild type. The mutant showed no activity after 10 min of pre-incubation at 50 °C, whereas the wild type SfamyR64 showed activity until 30 min of treatment. Sfamy appeared to have evolved earlier than its structural homolog. Conclusion: SfamyR64 N224 is crucial for enzyme activity and thermal stability. This glycosylation site is unique for fungal and bacterial α-amylases.

New Genes for Phylogenetic Studies of Lichenized Fungi: Glyceraldehyde-3-Phosphate Dehydrogenase and Beta-Tubulin Genes

2002 ◽  
Vol 34 (3) ◽  
pp. 237-246 ◽  
Author(s):  
Leena Myllys ◽  
Soili Stenroos ◽  
Arne Thell
Keyword(s):  
Ssu Rdna ◽  
Lichenized Fungi ◽  
Beta Tubulin ◽  
Data Set ◽  
Tubulin Genes ◽  
New Genes ◽  
Phylogenetic Studies ◽  
Pcr Product ◽  
Codon Positions ◽  
Relationship Of

AbstractPrimers for amplification and sequencing of partial glyceraldehyde-3-phosphate dehydrogenase (gpd) gene were designed for lichenized fungi. The 5’ gpd primer is most probably fungal specific, since a BLAST search in GenBank found identical sequences only from ascomycetous taxa, whereas the 3’ gpd primer was more universal. Utility of the gpd primers and previously designed beta-tubulin primers was tested in nine lichen taxa. Both the gpd and beta-tubulin primer pairs amplified in most of the taxa examined: the gpd primers generated a c. 1100 nucleotide fragment, whereas the PCR product obtained from the beta-tubulin primers was c. 900 nucleotides long. The gpd amplification products of Cladonia arbuscula and C. rangiferina were sequenced and both were found to contain three introns, the length of which varied between 49 to 83 nucleotides. To examine the applicability of gpd sequences in resolving relationships within Ascomycota, trees were calculated from 22 fungal gpd sequences obtained from GenBank together with the two Cladonia sequences using parsimony jackknifing. The gpd tree was compared with the SSU rDNA tree of the respective species (or genera). A similar analysis of the beta-tubulin gene was not performed, because only a few beta-tublin sequences from the same taxa were available in GenBank. The gpd tree was well resolved but in conflict with the SSU rDNA tree. In contrast to the SSU rDNA tree, the gpd tree did not support the monophyly of the Ascomycota. Analysis of the combined data set produced a tree very similar to that of the SSU rDNA data. However, the relationship of Lecanorales to the other orders remained unresolved. Even though gpd and beta-tubulin are highly conserved proteins, the third codon positions and introns are variable and both genes have the potential for inferring phylogenetic relationships at the lower taxonomic levels in the lichenized fungi. The two genes may be useful even below species level, depending on the species investigated.

scholarly journals Validation of Hosta alata (Asparagaceae) as a new species and its phylogenetic affinity

PhytoKeys ◽  
2021 ◽  
Vol 181 ◽  
pp. 79-93
Author(s):  
Tetsukazu Yahara ◽  
Shun K. Hirota ◽  
Kengo Fuse ◽  
Hiroyuki Sato ◽  
Shuichiro Tagane ◽  
...  
Keyword(s):  
New Species ◽  
Genotyping By Sequencing ◽  
Phylogenetic Affinity ◽  
Phylogenetic Studies ◽  
Genome Wide ◽  
Molecular Phylogenetic ◽  
Flowering Periods ◽  
Relationship Of ◽  
The Relationship ◽  
A New Species

Molecular phylogenetic studies of Hosta pulchella (Asparagaceae) and its relatives, which are native to Japan, have been conducted and resulted in a highly resolved phylogeny. Specifically, the relationship of H. pulchella to H. alata Hatusima, nom. nud. is investigated. These data include genome-wide SNPs obtained through conducting multiplexed ISSR genotyping by sequencing (MIG-seq). Based on these phylogenetic results, morphological observations, distribution, and differences in flowering periods of H. alata collections sympatric with H. pulchella, we find the two species closely related, but distinct. As such, we formally describe Hosta alatasp. nov. from the Oita Prefecture of Kyushu island, southwestern Japan.

scholarly journals Molecular Modeling of Cathepsin B protein in different Leishmania strains

2018 ◽  
Vol 8 (6-s) ◽  
pp. 224-226
Author(s):  
Jayprakash Mahato
Keyword(s):  
Protein Kinase ◽  
Cathepsin B ◽  
Phosphorylation Site ◽  
Three Dimensional ◽  
Cysteine Proteases ◽  
Glycosylation Site ◽  
Mammalian Host ◽  
Disulfide Bonding ◽  
Intracellular Protein Degradation ◽  
Kinase Phosphorylation

Cathepsin B like cysteine proteases representing a major component of the lysosomal proteolytic repertoire plays an important role in intracellular protein degradation. Comparative models of cathepsin B (CatB) protein of six different Leishmania strains were developed using MODELLER. The modeled three-dimensional (3-D) structure has the correct stereochemistry as gauged from the Ramachandran plot and good 3-D structure compatibility as assessed by PROCHECK and the DOPE score (DS2.1, Accelrys). The modeled proteins were energy minimized and validated using standard dynamic cascade protocol (DS 2.1). Seven different disulfide bonding sites are predicted in CatB protein of Leishmania. Two domains were identified and different motifs are present in catB protein of Leishmania like aspargine glycosylation site, protein kinase phosphorylation site, Protein kinase C activation site, N-myristoylation site. Considering that cathepsin B is essential for survival of Leishmania, including for virulence to the mammalian host, it may be viewed as an attractive drug target. Keyword: Molecular Modelling, Leishmania, Discover Studio, Protein Binding.   

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