scholarly journals Acquisition and Metastability of Centromere Identity and Function: Sequence Analysis of a Human Neocentromere

2000 ◽  
Vol 10 (6) ◽  
pp. 725-728 ◽  
Author(s):  
K. A. Maggert
Keyword(s):  
Sequence Analysis ◽  
And Function ◽  
Function Sequence

scholarly journals The Schizosaccharomyces pombe cho1+ Gene Encodes a Phospholipid Methyltransferase

Genetics ◽  
1998 ◽  
Vol 150 (2) ◽  
pp. 553-562
Author(s):  
Margaret I Kanipes ◽  
John E Hill ◽  
Susan A Henry
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Sequence Analysis ◽  
Schizosaccharomyces Pombe ◽  
Gene Disruption ◽  
Structure And Function ◽  
Biosynthetic Enzyme ◽  
Gene Encoding ◽  
Complementation Groups ◽  
Eukaryotic Organisms ◽  
And Function

Abstract The isolation of mutants of Schizosaccharomyces pombe defective in the synthesis of phosphatidylcholine via the methylation of phosphatidylethanolamine is reported. These mutants are choline auxotrophs and fall into two unlinked complementation groups, cho1 and cho2. We also report the analysis of the cho1+ gene, the first structural gene encoding a phospholipid biosynthetic enzyme from S. pombe to be cloned and characterized. The cho1+ gene disruption mutant (cho1Δ) is viable if choline is supplied and resembles the cho1 mutants isolated after mutagenesis. Sequence analysis of the cho1+ gene indicates that it encodes a protein closely related to phospholipid methyltransferases from Saccharomyces cerevisiae and rat. Phospholipid methyltransferases encoded by a rat liver cDNA and the S. cerevisiae OPI3 gene are both able to complement the choline auxotrophy of the S. pombe cho1 mutants. These results suggest that both the structure and function of the phospholipid N-methyltransferases are broadly conserved among eukaryotic organisms.

scholarly journals High-grade mutant OmpF induces decreased bacterial survival rate.

2014 ◽  
Vol 61 (2) ◽  
Author(s):  
Zhi-ping Zhao ◽  
Ting-ting Liu ◽  
Li Zhang ◽  
Min Luo ◽  
Xin Nie ◽  
...  
Keyword(s):  
Amino Acid ◽  
Survival Rate ◽  
Sequence Analysis ◽  
Amino Acid Sequence ◽  
Inhibition Zone ◽  
Structure And Function ◽  
High Grade ◽  
Bacterial Survival ◽  
Antibiotic Inhibition ◽  
And Function

OmpF plays very important roles in the influx of antibiotics and bacterial survival in the presence of antibiotics. However, high-grade mutant OmpF and its function in decreasing bacterial survival rate have not been reported to date. In the present study, we cloned a high-grade mutant OmpF (mOmpF) and sequence analysis suggested that over 45 percent of the DNA sequence was significantly mutated, leading to dramatic changes in over 55 percent of the amino acid sequence. mOmpF protein was successfully expressed. When grown in the presence of antibiotic, the bacterial survival rate decreased and the antibiotic inhibition zone became larger with the increase of the mOmpF. It was concluded that concentration of high-grade mutant mOmpF dramatically influenced the bacterial survival rate. The study presented here may provide insights into better understanding of the relationships between structure and function of OmpF.

scholarly journals The EVcouplings Python framework for coevolutionary sequence analysis

2018 ◽  
Author(s):  
Thomas A. Hopf ◽  
Anna G. Green ◽  
Benjamin Schubert ◽  
Sophia Mersmann ◽  
Charlotta P. I. Schäerfe ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
De Novo ◽  
Protein Complexes ◽  
Rapid Development ◽  
Sequence Alignments ◽  
Fully Integrated ◽  
Entry Level ◽  
Full Power ◽  
And Function ◽  
Python Package

AbstractSummaryCoevolutionary sequence analysis has become a commonly used technique for de novo prediction of the structure and function of proteins, RNA, and protein complexes. This approach requires extensive computational pipelines that integrate multiple tools, databases, and data processing steps. We present the EVcouplings framework, a fully integrated open-source application and Python package for coevolutionary analysis. The framework enables generation of sequence alignments, calculation and evaluation of evolutionary couplings (ECs), and de novo prediction of structure and mutation effects. The application has an easy to use command line interface to run workflows with user control over all analysis parameters, while the underlying modular Python package allows interactive data analysis and rapid development of new workflows. Through this multi-layered approach, the EVcouplings framework makes the full power of coevolutionary analyses available to entry-level and advanced users.Availabilityhttps://github.com/debbiemarkslab/[email protected], [email protected]

scholarly journals Unconventional conservation reveals structure-function relationships in the synaptonemal complex

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Lisa E Kursel ◽  
Henry D Cope ◽  
Ofer Rog
Keyword(s):  
Sequence Analysis ◽  
Synaptonemal Complex ◽  
Protein Evolution ◽  
Coiled Coil ◽  
Structural Features ◽  
Structure And Function ◽  
Coiled Coils ◽  
Functional Requirements ◽  
Coiled Coil Domain ◽  
And Function

Functional requirements constrain protein evolution, commonly manifesting in a conserved amino acid sequence. Here, we extend this idea to secondary structural features by tracking their conservation in essential meiotic proteins with highly diverged sequences. The synaptonemal complex (SC) is a ~100-nm-wide ladder-like meiotic structure present in all eukaryotic clades, where it aligns parental chromosomes and regulates exchanges between them. Despite the conserved ultrastructure and functions of the SC, SC proteins are highly divergent within Caenorhabditis. However, SC proteins have highly conserved length and coiled-coil domain structure. We found the same unconventional conservation signature in Drosophila and mammals, and used it to identify a novel SC protein in Pristionchus pacificus, Ppa-SYP-1. Our work suggests that coiled-coils play wide-ranging roles in the structure and function of the SC, and more broadly, that expanding sequence analysis beyond measures of per-site similarity can enhance our understanding of protein evolution and function.

scholarly journals Genetic and Sequence Analysis of the pTiC58 trb Locus, Encoding a Mating-Pair Formation System Related to Members of the Type IV Secretion Family

1998 ◽  
Vol 180 (23) ◽  
pp. 6164-6172 ◽  
Author(s):  
Pei-Li Li ◽  
Dawn M. Everhart ◽  
Stephen K. Farrand
Keyword(s):  
Sequence Analysis ◽  
Pair Formation ◽  
Type Iv Secretion ◽  
Ti Plasmid ◽  
Open Reading Frames ◽  
Conjugal Transfer ◽  
Mating Pair ◽  
Secretion Systems ◽  
Type Iv ◽  
And Function

ABSTRACT Conjugal transfer of pTiC58 requires two regions, trawhich contains the oriT and several genes involved in DNA processing and a region of undefined size and function that is located at the 2-o’clock position of the plasmid. Using transposon mutagenesis with Tn3HoHo1 and a binary transfer system, we delimited this second region, called trb, to an 11-kb interval between the loci for vegetative replication and nopaline catabolism. DNA sequence analysis of this region identified 13 significant open reading frames (ORFs) spanning 11,003 bp. The first, encodingtraI, already has been described and is responsible for the synthesis of Agrobacterium autoinducer (AAI) (I. Hwang, P.-L. Li, L. Zhang, K. R. Piper, D. M. Cook, M. E. Tate, and S. K. Farrand, Proc. Natl. Acad. Sci. USA 91:4639–4643, 1994). Translation products of the next 11 ORFs showed similarities to those of trbB, -C, -D,-E, -J, -K, -L,-F, -G, -H, and -I of the trb region of the octopine-type Ti plasmid pTi15955 and of the tra2 core region of RP4. In RP4, these genes encode mating-pair formation functions and are essential for the conjugal transfer of the IncP plasmid. Each of the trb gene homologues is oriented counterclockwise on the Ti plasmid. Expression of these genes, as measured by using the lacZ fusions formed by Tn3HoHo1, required the traI promoter and the transcriptional activator TraR along with its coinducer, AAI. While related to that of RP4, the trb system of pTiC58 did not allow propagation of the trb-specific bacteriophages PRD1, PRR1, and Pf3. The products of several trb genes of the Ti plasmid are similar to those of other loci that encode DNA transfer or protein secretion systems, all of which are members of the type IV secretion family.

A New Approach for Sequence Analysis

2011 ◽  
pp. 202-223 ◽  
Author(s):  
Kathryn Dempsey ◽  
Benjamin Currall ◽  
Richard Hallworth ◽  
Hesham Ali
Keyword(s):  
Sequence Analysis ◽  
Structure Function ◽  
Novel Structure ◽  
Structure Function Relationship ◽  
Function Relationship ◽  
And Function ◽  
Traditional Approaches ◽  
Pathological Disease ◽  
Relationship Of

Understanding the structure-function relationship of proteins offers the key to biological processes, and can offer knowledge for better investigation of matters with widespread impact, such as pathological disease and drug intervention. This relationship is dictated at the simplest level by the primary protein sequence. Since useful structures and functions are conserved within biology, a sequence with known structure-function relationship can be compared to related sequences to aid in novel structure-function prediction. Sequence analysis provides a means for suggesting evolutionary relationships, and inferring structural or functional similarity. It is crucial to consider these parameters while comparing sequences as they influence both the algorithms used and the implications of the results. For example, proteins that are closely related on an evolutionary time scale may have very similar structure, but entirely different functions. In contrast, proteins which have undergone convergent evolution may have dissimilar primary structure, but perform similar functions. This chapter details how the aspects of evolution, structure, and function can be taken into account when performing sequence analysis, and proposes an expansion on traditional approaches resulting in direct improvement of said analysis. This model is applied to a case study in the prestin protein and shows that the proposed approach provides a better understanding of input and output and can improve the performance of sequence analysis by means of motif detection software.

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