scholarly journals Species specific amino acid sequence–protein local structure relationships: An analysis in the light of a structural alphabet

2011 ◽  
Vol 276 (1) ◽  
pp. 209-217 ◽  
Author(s):  
Alexandre G. de Brevern ◽  
Agnel Praveen Joseph
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Local Structure ◽  
Structural Alphabet ◽  
Specific Amino Acid ◽  
Species Specific

PSD-93 mediate the dialogue between neuron and microglia and facilitate acute ischemic stroke by binding 357-395 amino acid sequence of CX3CL1

2020 ◽  
Author(s):  
Qingxiu Zhang ◽  
Lei He ◽  
Mo Chen ◽  
Hui Yang ◽  
Xiaowei Cao ◽  
...  
Keyword(s):  
Ischemic Stroke ◽  
Amino Acid ◽  
Amino Acid Sequence ◽  
Ischemia Reperfusion ◽  
Yeast Two Hybrid ◽  
Neuron Death ◽  
Specific Amino Acid ◽  
Ischemic Brain ◽  
Two Hybrid

Abstract Background: Our previous experiments demonstrated that PSD-93 mediates glutamate excitotoxicity induced by ischemic brain injury, which promotes the release of inflammatory cytokines in early ischemic brain injury by activating the NMDA receptor. Glutamate activity is the key to neuronal excitatory toxicity and microglial cell inflammatory response in the joints. However, the underlying mechanisms of how does PSD-93 mediate the dialogue between neurons and microglia in the postsynaptic dense region remain elusive. And CX3 chemokine ligand 1 (CX3CL1) is a chemokine that is specifically expressed in neurons. Its only receptor CX3CR1 is highly expressed in microglia and its main forms are membrane binding and soluble. In this study, we aim to clarify the specific amino acid sequence of the binding of psd-93 and CX3CL1 and investigate role of PSD-93 on regulating the crosstalk between neuron and microglia in acute ischemic stroke. Methods: In this study, male C57BL/6 mice aged 8-12 weeks and weighted 22-26g were applied with Middle Cerebral Artery Occlusion (MCAO) model and randomly divided into different groups. Firstly, co-immunoprecipitation and immunoblotting were used to detect the binding of PSD-93 and CX3CL1 at different time points 3h, 6h, 12h 24h, 48h and 72h following cerebral ischemic/reperfusion. Meanwhile, ELISA was used to investigate the expression of soluble CX3CL1 at the same time points to confirm the relationship between of the expression of soluble CX3CL1 and the combination of PSD-93 and CX3CL1. Secondly, two bait plasmids pSos-PSD-93-full length, pSos-CX3CL1-full length and five mutant plasmids: pMyr-PSD-93-mut1, pMyr-PSD-93-mut2, pMyr-PSD-93-mut3, pMyr-PSD-93-mut4, and pMyr-CX3CL1-mut, were constructed and used a yeast two-hybrid system to screen and identify positive clones and to determine the sequence in which the two proteins bind to each other. Thirdly, the proteins corresponding to the three positive clones obtained in the yeast two-hybrid experiment were used to construct plasmids for transfection of eukaryotic cells and the protein expression binding was verified again by in vitro co-immunoprecipitation. Finally, a specific fusion small peptide Tat-CX3CL1 were designed according to above experiment to inhibit the integration of PSD-93 and CX3CL1 and to explore their role on neuron death following reperfusion. Results: We found that the binding capacity of PSD-93 and CX3CL1 proteins peaked at 6h after ischemia/reperfusion and then decreased gradually. The specific amino acid sequence of PSD-93 and CX3CL1 binding was obtained by yeast double hybridization and in vitro immunoprecipitation. We identified that their binding sites are located in the 420-535 amino acid sequence of PSD-93 and 357-395 amino acid sequence of CX3CL1. And a specific fusion small peptide Tat-CX3CL1 (357-395aa) were designed to inhibit the integration of PSD-93 and CX3CL1 and perform neuroprotection on neuron death following reperfusion. Conclusions: Our results suggest that PSD-93 promotes the formation of its soluble form by binding to CX3CL1, which is recruited to the surface of microglia to bind to CX3CR1, thereby activating microglia to initiate inflammation. Thus, specific blockade of PSD-93-CX3CL1 coupling can reduce ischemia-reperfusion induced neuronal cell death, which provide a new target to treat ischemic stroke.

scholarly journals Amino acid sequence variations in Nicotiana CRR4 orthologs determine the species-specific efficiency of RNA editing in plastids

2008 ◽  
Vol 36 (19) ◽  
pp. 6155-6164 ◽  
Author(s):  
Kenji Okuda ◽  
Yuya Habata ◽  
Yoshichika Kobayashi ◽  
Toshiharu Shikanai
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Rna Editing ◽  
Sequence Variations ◽  
Species Specific

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

2009 ◽  
Vol 91 (2) ◽  
pp. 101-109 ◽  
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.

scholarly journals Purification, Characterization, and Molecular Analysis of the Gene Encoding Glucosyltransferase fromStreptococcus oralis

2000 ◽  
Vol 68 (5) ◽  
pp. 2475-2483 ◽  
Author(s):  
Taku Fujiwara ◽  
Tomonori Hoshino ◽  
Takashi Ooshima ◽  
Shizuo Sobue ◽  
Shigeyuki Hamada
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Pcr Primers ◽  
Water Soluble ◽  
Oral Streptococci ◽  
Amino Acid Residues ◽  
Gene Encoding ◽  
Streptococcus Sanguis ◽  
Specific Nucleotide Sequence ◽  
Species Specific

ABSTRACT Streptococcus oralis is a member of the oral streptococcal family and an early-colonizing microorganism in the oral cavity of humans. S. oralis is known to produce glucosyltransferase (GTase), which synthesizes glucans from sucrose. The enzyme was purified chromatographically from a culture supernatant of S. oralis ATCC 10557. The purified enzyme, GTase-R, had a molecular mass of 173 kDa and a pI of 6.3. This enzyme mainly synthesized water-soluble glucans with no primer dependency. The addition of GTase markedly enhanced the sucrose-dependent resting cell adhesion of Streptococcus mutans at a level similar to that found in growing cells of S. mutans. The antibody against GTase-R inhibited the glucan-synthesizing activities ofStreptococcus gordonii and Streptococcus sanguis, as well as S. oralis. The N-terminal amino acid sequence of GTase-R exhibited no similarities to known GTase sequences of oral streptococci. Using degenerate PCR primers, an 8.1-kb DNA fragment, carrying the gene (gtfR) coding for GTase-R and its regulator gene (rgg), was cloned and sequenced. Comparison of the deduced amino acid sequence revealed that thergg genes of S. oralis and S. gordonii exhibited a close similarity. The gtfR gene was found to possess a species-specific nucleotide sequence corresponding to the N-terminal 130 amino acid residues. Insertion oferm or aphA into the rgg orgtfR gene resulted in decreased GTase activity by the organism and changed the colony morphology of these transformants. These results indicate that S. oralis GTase may play an important role in the subsequent colonizing of mutans streptoccoci.

scholarly journals New Species Genetic Approach To Identify Strains of Mitis Group Streptococci That Are Donors of Rifampin Resistance toStreptococcus pneumoniae

2010 ◽  
Vol 55 (1) ◽  
pp. 368-372 ◽  
Author(s):  
María-José Ferrándiz ◽  
Carmen Ardanuy ◽  
Josefina Liñares ◽  
Luz Balsalobre ◽  
María Teresa García ◽  
...  
Keyword(s):  
Amino Acid ◽  
Single Amino Acid ◽  
Rrna Gene ◽  
Specific Amino Acid ◽  
Sequence Characterization ◽  
Rifampin Resistance ◽  
Species Specific ◽  
Amino Acid Signature ◽  
Type Strains

ABSTRACTEight rifampin-resistant streptococci of the mitis group were identified at the species level by using a concatenated 16S rRNA gene-sodA-rpoB-hlpAsequence. Characterization of theirrpoBalleles showed single amino acid changes involved in rifampin resistance. Comparison of RpoB sequences from pneumococcal recombinant isolates, viridans isolates, and type strains revealed a species-specific amino acid signature, which allowed it to be ascertained that recombinant RpoBs were originated in genetic interchanges withStreptococcus mitisandStreptococcus oralis.

scholarly journals Identification of 14-α-Lanosterol Demethylase (CYP51) in Scedosporium Species

2018 ◽  
Vol 62 (8) ◽  
Author(s):  
Anne Bernhardt ◽  
Wieland Meyer ◽  
Volker Rickerts ◽  
Toni Aebischer ◽  
Kathrin Tintelnot
Keyword(s):  
Amino Acid ◽  
Resistance Mechanisms ◽  
Upstream Region ◽  
Scedosporium Apiospermum ◽  
Gene Encoding ◽  
Specific Amino Acid ◽  
Content Type ◽  
Scedosporium Dehoogii ◽  
Lanosterol Demethylase ◽  
Species Specific

ABSTRACT Scedosporium spp. cause infections (scedosporiosis) in both immunocompetent and immunocompromised individuals and may persistently colonize the respiratory tract in patients with cystic fibrosis (CF). They are less susceptible against azoles than are other molds, such as Aspergillus spp., suggesting the presence of resistance mechanisms. It can be hypothesized that the decreased susceptibility of Scedosporium spp. to azoles is also CYP51 dependent. Analysis of the Scedosporium apiospermum and Scedosporium aurantiacum genomes revealed one CYP51 gene encoding the 14-α-lanosterol demethylase. This gene from 159 clinical or environmental Scedosporium isolates and three Lomentospora prolificans isolates has been sequenced and analyzed. The Scedosporium CYP51 protein clustered with the group of known CYP51B orthologues and showed species-specific polymorphisms. A tandem repeat in the 5′ upstream region of Scedosporium CYP51 like that in Aspergillus fumigatus could not be detected. Species-specific amino acid alterations in CYP51 of Scedosporium boydii, Scedosporium ellipsoideum, Scedosporium dehoogii, and Scedosporium minutisporum isolates were located at positions that have not been described as having an impact on azole susceptibility. In contrast, two of the three S. apiospermum-specific amino acid changes (Y136F and G464S) corresponded to respective mutations in A. fumigatus CYP51A at amino acid positions 121 and 448 (Y121F and G448S, respectively) that had been linked to azole resistance.

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