scholarly journals Combination of multiple alignment analysis and surface mapping paves a way for a detailed pathway reconstruction--The case of VHL (von Hippel-Lindau) protein and angiogenesis regulatory pathway

2004 ◽  
Vol 13 (3) ◽  
pp. 786-796 ◽  
Author(s):  
S. Sikora
Keyword(s):  
Multiple Alignment ◽  
Regulatory Pathway ◽  
Surface Mapping ◽  
Von Hippel Lindau ◽  
Pathway Reconstruction ◽  
Multiple Alignment Analysis ◽  
Alignment Analysis

scholarly journals Structure of CARB-4 and AER-1 CarbenicillinHydrolyzing β-Lactamases

1998 ◽  
Vol 42 (8) ◽  
pp. 1966-1972 ◽  
Author(s):  
François Sanschagrin ◽  
Noureddine Bejaoui ◽  
Roger C. Levesque
Keyword(s):  
Amino Acids ◽  
Pseudomonas Aeruginosa ◽  
Dna Sequences ◽  
Active Site ◽  
Multiple Alignment ◽  
Dna Homology ◽  
Class A ◽  
Canonical Amino Acid ◽  
Multiple Alignment Analysis ◽  
Alignment Analysis

ABSTRACT We determined the nucleotide sequences ofblaCARB-4 encoding CARB-4 and deduced a polypeptide of 288 amino acids. The gene was characterized as a variant of group 2c carbenicillin-hydrolyzing β-lactamases such as PSE-4, PSE-1, and CARB-3. The level of DNA homology between thebla genes for these β-lactamases varied from 98.7 to 99.9%, while that between these genes andblaCARB-4 encoding CARB-4 was 86.3%. TheblaCARB-4 gene was acquired from some other source because it has a G+C content of 39.1%, compared to a G+C content of 67% for typical Pseudomonas aeruginosa genes. DNA sequencing revealed that blaAER-1 shared 60.8% DNA identity with blaPSE-3 encoding PSE-3. The deduced AER-1 β-lactamase peptide was compared to class A, B, C, and D enzymes and had 57.6% identity with PSE-3, including an STHK tetrad at the active site. For CARB-4 and AER-1, conserved canonical amino acid boxes typical of class A β-lactamases were identified in a multiple alignment. Analysis of the DNA sequences flankingblaCARB-4 and blaAER-1 confirmed the importance of gene cassettes acquired via integrons inbla gene distribution.

scholarly journals A putative effector UvHrip1 inhibits BAX-triggered cell death in Nicotiana benthamiana, and infection of Ustilaginoidea virens suppresses defense-related genes expression

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9354
Author(s):  
Yingling Wang ◽  
Jing Li ◽  
Shibo Xiang ◽  
Jianming Zhou ◽  
Xunwen Peng ◽  
...  
Keyword(s):  
Nicotiana Benthamiana ◽  
Plant Immunity ◽  
Plant Cells ◽  
Multiple Alignment ◽  
Ustilaginoidea Virens ◽  
Gfp Fusion Protein ◽  
Genes Expression ◽  
False Smut ◽  
Multiple Alignment Analysis ◽  
Alignment Analysis

Rice false smut (RFS), caused by Ustilaginoidea virens, is one of the most detrimental rice fungal diseases and pose a severe threat to rice production and quality. Effectors in U. virens often act as a set of essential virulence factors that play crucial roles in the interaction between host and the pathogen. Thus, the functions of each effector in U. virens need to be further explored. Here, we performed multiple alignment analysis and demonstrated a small secreted hypersensitive response-inducing protein (hrip), named UvHrip1, was highly conserved in fungi. The predicted SP of UvHrip1 was functional, which guided SUC secreted from yeast and was recognized by plant cells. The localization of UvHrip1 was mainly in the nucleus and cytoplasm monitored through the GFP fusion protein in Nicotiana benthamiana cells. uvhrip1 was drastically up-regulated in the susceptible cultivar LYP9 of rice during the pathogen infection, while did not in the resistant cultivar IR28. We also proved that UvHrip1 suppressed the mammalian BAX-induced necrosis-like defense symptoms in N. benthamiana. Furthermore, patterns of expression of defense-related genes, OsPR1#012 and OsPR10b, were regulated over U. virens infection in rice. Collectively, our data demonstrated that infection of U. virens suppresses defense-related genes expression and UvHrip1 was most likely a core effector in regulating plant immunity.

Comparative analysis of ITS1 nucleotide sequence reveals distinct genetic difference between Brugia malayi from Northeast Borneo and Thailand

Parasitology ◽  
2012 ◽  
Vol 140 (1) ◽  
pp. 39-45 ◽  
Author(s):  
MUN-YIK FONG ◽  
RAHMAH NOORDIN ◽  
YEE-LING LAU ◽  
FEI-WEN CHEONG ◽  
MUHAMMAD HAFIZNUR YUNUS ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Genetic Difference ◽  
Brugia Malayi ◽  
Wide Distribution ◽  
Multiple Alignment ◽  
Molecular Techniques ◽  
Human Blood Samples ◽  
Multiple Alignment Analysis ◽  
Alignment Analysis ◽  
Parasitic Worms

SUMMARYBrugia malayi is one of the parasitic worms which causes lymphatic filariasis in humans. Its geographical distribution includes a large part of Asia. Despite its wide distribution, very little is known about the genetic variation and molecular epidemiology of this species. In this study, the internal transcribed spacer 1 (ITS1) nucleotide sequences of B. malayi from microfilaria-positive human blood samples in Northeast Borneo Island were determined, and compared with published ITS1 sequences of B. malayi isolated from cats and humans in Thailand. Multiple alignment analysis revealed that B. malayi ITS1 sequences from Northeast Borneo were more similar to each other than to those from Thailand. Phylogenetic trees inferred using Neighbour-Joining and Maximum Parsimony methods showed similar topology, with 2 distinct B. malayi clusters. The first cluster consisted of Northeast Borneo B. malayi isolates, whereas the second consisted of the Thailand isolates. The findings of this study suggest that B. malayi in Borneo Island has diverged significantly from those of mainland Asia, and this has implications for the diagnosis of B. malayi infection across the region using ITS1-based molecular techniques.

MALAKITE: AN AUTOMATIC TOOL FOR CHARACTERISATION OF STRUCTURE OF RELIABLE BLOCKS IN MULTIPLE ALIGNMENTS OF PROTEIN SEQUENCES

2010 ◽  
Vol 08 (03) ◽  
pp. 503-517 ◽  
Author(s):  
BORIS BURKOV ◽  
BORIS NAGAEV ◽  
SERGEI SPIRIN ◽  
ANDREI ALEXEEVSKI
Keyword(s):  
Protein Sequences ◽  
Structural Data ◽  
Multiple Alignment ◽  
Multiple Alignments ◽  
Simple Consideration ◽  
Automatic Tool ◽  
Alignment Analysis

It makes sense to speak of alignment of protein sequences only within the regions, where the sequences are related to each other. This simple consideration is often disregarded by programs of multiple alignment construction. A package for alignment analysis MAlAKiTE (Multiple Alignment Automatic Kinship Tiling Engine) is introduced. It aims to find the blocks of reliable alignment, which contain related regions only, within the whole alignment and allows for dealing with them. The validity of the detection of reliable blocks' was verified by comparison with structural data.

Evaluating the specificity of primers employed for PCR-based diagnostics of Leishmaniases using multiple alignment analysis

2013 ◽  
Vol 35 (85) ◽  
Author(s):  
Jane Eyre Gabriel
Keyword(s):  
Parasite Species ◽  
Leishmania Species ◽  
Nematostella Vectensis ◽  
Sequence Annotation ◽  
Biological Sequence ◽  
Annotation Database ◽  
Sequence Search ◽  
Target Templates ◽  
Multiple Alignment Analysis ◽  
Alignment Analysis

The purpose of this study was to assess the specificity of distinct primers used in the molecular diagnosis for Leishmania detection by using biological sequence search and alignment tools. Four primer pairs routinely employed in the PCR-based diagnostics for Leishmaniasis detection were evaluated through the software Primer-BLAST, which compares nucleotide sequences against user-selected database to avoid primer pairs cause non-specific amplifications. The LU5A-LB3C primer pair showed good specificity among all primers analyzed, generating alignments exclusively against distinct sequences of Leishmania species and no matches were found with other parasite species. Whereas the primer pairs designated MP3H - MP1L, B1-B2 and 13A-13B demonstrated matches against distinct sequences of Leishmania strains and other species, such as Rhesus monkey (Macaca mulatta) and starlet sea anemone (Nematostella vectensis). These findings emphasize the importance of selecting suitable primers for diagnosis of molecular diseases by conducting previous screenings in order to infer their specificity and identity against target templates within biological sequence annotation database.

scholarly journals Structural Similarity Analysis of Spike Proteins of SARS-CoV-2 and Other SARS-related Coronaviruses

2020 ◽  
Author(s):  
YoungJoon Park ◽  
Ju Won Ahn ◽  
Sojung Hwang ◽  
Kyoung Su Sung ◽  
Jaejoon Lim ◽  
...  
Keyword(s):  
Amino Acid ◽  
Three Dimensional ◽  
Structural Similarity ◽  
Amino Acid Sequences ◽  
Dimensional Structure ◽  
Web Based ◽  
S Protein ◽  
Multiple Alignment Analysis ◽  
Horseshoe Bat ◽  
Alignment Analysis

Objectives Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has high infectivity in humans, attributed to the strong affinity of its spike (S) protein to human angiotensin-converting enzyme 2 (ACE2). Here, we analyzed the structural similarity of the S protein between SARS-CoV-2 and other SARS-related coronaviruses (CoVs). Methods We performed multiple alignment analysis of nine amino acid sequences of CoV S proteins from NCBI with MAFFT web-based software, followed by phylogeny analysis. Three-dimensional structure modeling was performed by SWISS-MODEL. We calculated the template modeling score between the S protein of SARS-CoV-2 and that of other SARS-related CoVs. Results The S1 domain of the unclassified CoV RaTG13 (the host of which is the intermediate horseshoe bat) was structurally very similar to that of SARS-CoV-2, implying that RaTG13 could be the origin of SARS-CoV-2. In addition, the folding property of the entire S protein was nearly the same between SARS-CoV-2 and RaTG13 after the PRRA amino acid insertion was removed from SARS-CoV-2. Conclusions RaTG13 could have a high binding affinity to ACE2, similar to SARS-CoV-2, and it is therefore highly likely to infect other animals. Therefore, massive research and monitoring of CoVs in animals is necessary to prevent future COVID-19-like disasters.

scholarly journals Molecular characterisation and expression analysis of scavenger receptor class B member 1 (SR-B1) gene in Nile tilapia Oreochromis niloticus (Linnaeus, 1758)

2019 ◽  
Vol 66 (2) ◽  
Author(s):  
Yucong Huang ◽  
Shuanghu Cai
Keyword(s):  
Oreochromis Niloticus ◽  
Nile Tilapia ◽  
Scavenger Receptor ◽  
Pcr Analysis ◽  
Real Time Quantitative Pcr ◽  
Scavenger Receptor Class ◽  
B1 Gene ◽  
Class B ◽  
Multiple Alignment Analysis ◽  
Alignment Analysis

The scavenger receptor class B member 1 (SR-B1) plays an important role in the first level of host defense against invading pathogens. In the present study, we cloned and characterized SR-B1 gene from Oreochromis niloticus (Linnaeus, 1758). The sequence of SR-B1 is 2248-bp long and contains a 1404-bp ORF encoded 467 amino acids. The sequence alignment showed that SR-B1 gene contains ten exons and nine introns. A multiple alignment analysis suggested that SR-B1 protein contains the conserved CXXS redox and GXXXG motifs, and shared high similarities with that of other species. On a phylogenetic tree, SR-B1 clustered with those of other teleosts and formed a separate fish clade. Real-time quantitative PCR analysis showed that SR-B1 was differentially expressed in various tissues and the expression levels in spleen and intestine were significantly upregulated by Streptococcus agalactiae infection. The results suggest that SR-B1 may be involved in the immune response against bacteria in Nile tilapia.

Cloning and expression of delta-1-pyrroline-5-carboxylate dehydrogenase in Escherichia coli DH5α improves phosphate solubilization

2014 ◽  
Vol 60 (11) ◽  
pp. 761-765 ◽  
Author(s):  
Mingbo Gong ◽  
Chaoxi Tang ◽  
Changxiong Zhu
Keyword(s):  
Escherichia Coli ◽  
Organic Acid ◽  
Sole Source ◽  
Penicillium Oxalicum ◽  
Cloning And Expression ◽  
Soluble Phosphate ◽  
Reading Frame ◽  
Multiple Alignment Analysis ◽  
Phosphate Solubilizing ◽  
Alignment Analysis

A primary cDNA library of Penicillium oxalicum I1 was constructed using the switching mechanism at the 5′ end of the RNA transcript (SMART) technique. A total of 106 clones showed halos in tricalcium phosphate (TCP) medium, and clone I-40 showed clear halos. The full-length cDNA of clone I-40 was 1355 bp with a complete open reading frame (ORF) of 1032 bp, encoding a protein of 343 amino acids. Multiple alignment analysis revealed a high degree of homology between the ORF of clone I-40 and delta-1-pyrroline-5-carboxylate dehydrogenase (P5CDH) of other fungi. The ORF expression vector was constructed and transformed into Escherichia coli DH5α. The transformant (ORF-1) with the P5CDH gene secreted organic acid in medium with TCP as the sole source of phosphate. Acetic acid and α-ketoglutarate were secreted in 4 and 24 h, respectively. ORF-1 decreased the pH of the medium from 6.62 to 3.45 and released soluble phosphate at 0.172 mg·mL−1 in 28 h. Expression of the P. oxalicum I1 p5cdh gene in E. coli could enhance organic acid secretion and phosphate-solubilizing ability.

scholarly journals MYB transcription factor CiMYB42 regulates limonoids biosynthesis in citrus

2020 ◽  
Author(s):  
pan zhang ◽  
Xiaofeng Liu ◽  
Xin Xu ◽  
Fusheng Wang ◽  
Junhong Long ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Biosynthetic Pathway ◽  
Developmental Stages ◽  
Regulatory Mechanisms ◽  
Myb Transcription Factor ◽  
Transcription Activator ◽  
Multiple Alignment Analysis ◽  
Citrus Varieties ◽  
Alignment Analysis

Abstract Backgrounds Limonoids, a major bioactive components, are produced by triterpenoids metabolic pathway. So far, the detailed biochemical reactions regarding to limonoid biosynthesis and their molecular regulation remain elusive. The identification of transcription factors that regulate limonoids biosynthetic pathways is not only necessary for understanding the regulatory mechanisms but also as a tool for manipulating biosynthetic genes for biotechnological applications.Results In this study, CiMYB42 transcription factor was isolated and identified. Multiple alignment analysis and phylogenetic analysis demonstrated that CiMYB42 is a typical R2R3MYB transcription factor and its amino acid is similar to that of AtMYB42 . The limonoids content was higher in the citrus sinensis and citrus grandis than other species. The diverse accumulation patterns also showed in different leaf developmental stages. Expression of CiMYB42 was significantly related to limonoids content and the expression of CiOSC in some of citrus varieties. CiMYB42 transgenic sweet orange resulted significantly change on limonoids contents. Noticeably, CiMYB42 -RNAi induced dwarf phenotype and mainly decreased nomilin accumulation. Overexpressing CiMYB42 mainly increased limonin content. Yeast one hybrid assay results indicated that CiMYB42 exclusively bind to the promoter of CiOSC. In brief, CiMYB42 involved in the limonoids biosynthesis through binding the promoter of CiOSC in citrus.Conclusions These results indicated that CiMYB42 is an important transcription activator involved in limonoids biosynthesis by regulating the expression of CiOSC . This is the first report elucidating the role of transcription factor in citrus limonoids biosynthesis. Our contributions will provide a reference to understanding regulatory mechanisms of R2R3MYB TFs in the triterpenoids biosynthetic pathway.

Sign in / Sign up

Export Citation Format

Share Document