12364
2012
eng
97-128
6
article
1
2015-12-21
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Different evolutionary modifications as a guide to rewire two-component systems
Two-component systems (TCS) are short signalling pathways generally occurring in prokaryotes. They frequently regulate prokaryotic stimulus responses and thus are also of interest for engineering in biotechnology and synthetic biology. The aim of this study is to better understand and describe rewiring of TCS while investigating different evolutionary scenarios. Based on large-scale screens of TCS in different organisms, this study gives detailed data, concrete alignments, and structure analysis on three general modification scenarios, where TCS were rewired for new responses and functions: (i) exchanges in the sequence within single TCS domains, (ii) exchange of whole TCS domains; (iii) addition of new components modulating TCS function. As a result, the replacement of stimulus and promotor cassettes to rewire TCS is well defined exploiting the alignments given here. The diverged TCS examples are non-trivial and the design is challenging. Designed connector proteins may also be useful to modify TCS in selected cases.
Bioinformatics and Biology Insights
PMC3348925
10.4137/BBI.S9356
urn:nbn:de:bvb:20-opus-123647
This is an open access article. Unrestricted non-commercial use is permitted provided the original work is properly cited.
Bioinformatics and Biology Insights 2012:6 97–128. doi: 10.4137/BBI.S9356
Beate Krueger
Torben Friedrich
Frank Förster
Jörg Bernhardt
Roy Gross
Thomas Dandekar
eng
uncontrolled
histidine kinase
eng
uncontrolled
connector
eng
uncontrolled
Mycoplasma
eng
uncontrolled
engineering
eng
uncontrolled
promoter
eng
uncontrolled
sensor
eng
uncontrolled
response regulator
eng
uncontrolled
synthetic biology
eng
uncontrolled
sequence alignment
Datenverarbeitung; Informatik
Biowissenschaften; Biologie
open_access
Theodor-Boveri-Institut für Biowissenschaften
Universität Würzburg
https://opus.bibliothek.uni-wuerzburg.de/files/12364/f_3168-BBI-Different-Evolutionary-Modifications-as-a-Guide-to-Rewire-Two-Componen.pdf_4288.pdf
12460
2012
eng
e3806
61
article
1
2016-01-19
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The ITS2 Database
The internal transcribed spacer 2 (ITS2) has been used as a phylogenetic marker for more than two decades. As ITS2 research mainly focused on the very variable ITS2 sequence, it confined this marker to low-level phylogenetics only. However, the combination of the ITS2 sequence and its highly conserved secondary structure improves the phylogenetic resolution1 and allows phylogenetic inference at multiple taxonomic ranks, including species delimitation.
The ITS2 Database presents an exhaustive dataset of internal transcribed spacer 2 sequences from NCBI GenBank accurately reannotated. Following an annotation by profile Hidden Markov Models (HMMs), the secondary structure of each sequence is predicted. First, it is tested whether a minimum energy based fold (direct fold) results in a correct, four helix conformation. If this is not the case, the structure is predicted by homology modeling. In homology modeling, an already known secondary structure is transferred to another ITS2 sequence, whose secondary structure was not able to fold correctly in a direct fold.
The ITS2 Database is not only a database for storage and retrieval of ITS2 sequence-structures. It also provides several tools to process your own ITS2 sequences, including annotation, structural prediction, motif detection and BLAST search on the combined sequence-structure information. Moreover, it integrates trimmed versions of 4SALE and ProfDistS for multiple sequence-structure alignment calculation and Neighbor Joining tree reconstruction. Together they form a coherent analysis pipeline from an initial set of sequences to a phylogeny based on sequence and secondary structure.
In a nutshell, this workbench simplifies first phylogenetic analyses to only a few mouse-clicks, while additionally providing tools and data for comprehensive large-scale analyses.
Journal of Visual Expression
10.3791/3806
urn:nbn:de:bvb:20-opus-124600
Journal of Visual Expression (61), e3806, doi:10.3791/3806 (2012)
Benjamin Merget
Christian Koetschan
Thomas Hackl
Frank Förster
Thomas Dandekar
Tobias Müller
Jörg Schultz
Matthias Wolf
eng
uncontrolled
homology modeling
eng
uncontrolled
molecular systematics
eng
uncontrolled
internal transcribed spacer 2
eng
uncontrolled
alignment
eng
uncontrolled
genetics
eng
uncontrolled
secondary structure
eng
uncontrolled
ribosomal RNA
eng
uncontrolled
phylogenetic tree
eng
uncontrolled
phylogeny
Datenverarbeitung; Informatik
Chemie und zugeordnete Wissenschaften
Biowissenschaften; Biologie
open_access
Theodor-Boveri-Institut für Biowissenschaften
Institut für Pharmazie und Lebensmittelchemie
Universität Würzburg
https://opus.bibliothek.uni-wuerzburg.de/files/12460/jove-61-3806.pdf
13444
2012
eng
e45682
9
7
article
1
2016-06-06
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Comparative proteome analysis of Milnesium tardigradum in early embryonic state versus adults in active and anhydrobiotic state
Tardigrades have fascinated researchers for more than 300 years because of their extraordinary capability to undergo cryptobiosis and survive extreme environmental conditions. However, the survival mechanisms of tardigrades are still poorly understood mainly due to the absence of detailed knowledge about the proteome and genome of these organisms. Our study was intended to provide a basis for the functional characterization of expressed proteins in different states of tardigrades. High-throughput, high-accuracy proteomics in combination with a newly developed tardigrade specific protein database resulted in the identification of more than 3000 proteins in three different states: early embryonic state and adult animals in active and anhydrobiotic state. This comprehensive proteome resource includes protein families such as chaperones, antioxidants, ribosomal proteins, cytoskeletal proteins, transporters, protein channels, nutrient reservoirs, and developmental proteins. A comparative analysis of protein families in the different states was performed by calculating the exponentially modified protein abundance index which classifies proteins in major and minor components. This is the first step to analyzing the proteins involved in early embryonic development, and furthermore proteins which might play an important role in the transition into the anhydrobiotic state.
PLoS One
10.1371/journal.pone.0045682
urn:nbn:de:bvb:20-opus-134447
PLoS ONE 7(9): e45682. doi:10.1371/journal.pone.0045682
Elham Schokraie
Uwe Warnken
Agnes Hotz-Wagenblatt
Markus A. Grohme
Steffen Hengherr
Frank Förster
Ralph O. Schill
Marcus Frohme
Thomas Dandekar
Martina Schnölzer
eng
uncontrolled
life-span regulation
eng
uncontrolled
genes
eng
uncontrolled
Yolk protein
eng
uncontrolled
water stress
eng
uncontrolled
expression
eng
uncontrolled
tolerance
eng
uncontrolled
richtersius coronifer
eng
uncontrolled
superoxide-dismutase
eng
uncontrolled
caenorhabditis elegans
eng
uncontrolled
arabidopsis thaliana
eng
uncontrolled
vitellogenin
Datenverarbeitung; Informatik
Biowissenschaften; Biologie
open_access
Theodor-Boveri-Institut für Biowissenschaften
Universität Würzburg
https://opus.bibliothek.uni-wuerzburg.de/files/13444/Schokraie_PLoSOne.pdf