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Bacterial computing with engineered populations.

We describe strategies for the construction of bacterial computing platforms by describing a number of results from the recently completed bacterial computing with engineered populations project. In...read more

author M.Amos, I.M. Axmann, N. Blüthgen, F. de la Cruz, A. Jaramillo, A. Rodriques-Paton, F. Simmel
publication Philos Trans A Math Phys Eng Sci
date 2015
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Daily expression pattern of protein-encoding genes and small noncoding RNAs in Synechocystis sp. strain PCC 6803.

Many organisms harbor circadian clocks with periods close to 24 h. These cellular clocks allow organisms to anticipate the environmental cycles of day and night by synchronizing circadian rhythms with...read more

author C. Beck, S. Hertel, A. Rediger, R. Lehmann, A. Wiegard, A. Kölsch, B. Heilmann, J. Georg, W.R. Hess,  I.M. Axmann
publication Appl Environ Microbiol.
date 2014
download http://www.ncbi.nlm.nih.gov/pubmed/24928881

Daily rhythms in the cyanobacterium synechococcus elongatus probed by high-resolution mass spectrometry-based proteomics reveals a small defined set of cyclic proteins.

 Circadian rhythms are self-sustained and adjustable cycles, typically entrained with light/dark and/or temperature cycles. These rhythms are present in animals, plants, fungi, and several bacteria....read more

author A.C. Guerreiro, M. Benevento, R. Lehmann, B. van Breukelen, H. Post, P. Giansanti, A.F. Maarten Altelaar, I.M. Axmann, A.J. Heck
publication Mol Cell Proteomics
date 2014
download http://www.ncbi.nlm.nih.gov/pubmed/24677030

Insight into cyanobacterial circadian timing from structural details of the KaiB-KaiC interaction.

Circadian timing in cyanobacteria is determined by the Kai system consisting of KaiA, KaiB, and KaiC. Interactions between Kai proteins change the phosphorylation status of KaiC, defining the phase of...read more

author J. Snijder, R.J. Burnley, A. Wiegard, A.S. Melquiond, A.M. Bonvin, I.M. Axmann, A.J. Heck
publication Proc Natl Acad Sci USA
date 2014
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http://www.ncbi.nlm.nih.gov/pubmed/24474762


Diversity of KaiC-based timing systems in marine Cyanobacteria

The coordination of biological activities into daily cycles provides an important advantage for the fitness of diverse organisms. Most eukaryotes possess an internal clock ticking with a...read more

author I.M. Axmann, S. Hertel, A. Wiegard, A.K. Dörrich, A. Wilde
publication Marine Genomics
date 2014
download http://www.sciencedirect.com/science/article/pii/S1874778713000858#

Multiple Checkpoints for the Expression of the Chloroplast-Encoded Splicing Factor MatK

The chloroplast genome of land plants contains only a single gene for a splicing factor, Maturase K (MatK). To better understand the regulation of matK gene expression, we quantitatively...read more

author S. Hertel, R. Zoschke, L. Neumann, Q. Yujiao, I.M. Axmann, C. Schmitz-Linneweber
publication Plant Physiology
date 2013
download http://www.plantphysiol.org/content/163/4/1686.long

How cyanobacteria pose new problems to old methods: challenges in microarray time series analysis

Background The transcriptomes of several cyanobacterial strains have been shown to exhibit diurnal oscillation patterns reflecting the diurnal phototrophic lifestyle of the organisms. ...read more

author R. Lehmann, R. Machné, J. Georg, M. Benary, I.M. Axmann, R. Steuer
publication BMC Bioinformatics
date 2013
download http://www.biomedcentral.com/1471-2105/14/133

Revealing a Two-Loop Transcriptional Feedback Mechanism in the Cyanobacterial Circadian Clock

Molecular genetic studies in the circadian model organism Synechococcus have revealed that the KaiC protein, the central component of the circadian clock in cyanobacteria, is involved in...read more

author S. Hertel, C. Brettschneider, I.M. Axmann
publication PLoS Computational Biology
date 2013
download http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002966

Biochemical analysis of three putative KaiC clock proteins from Synechocystis sp. PCC 6803 suggests their functional divergence.

Cyanobacteria were shown to have a circadian clock system that consists of mainly three protein components: KaiA, KaiB and KaiC. This system is well understood in the cyanobacterium Synechococcus...read more

author A. Wiegard, A.K. Dörrich, H. Deinzer, C. Beck, A. Wilde, J. Holtzendorff, I.M. Axmann
publication Microbiology
date 2013
download http://www.ncbi.nlm.nih.gov/pubmed/23449916?dopt=Abstract

6S RNA - an old issue became blue-green.

6S RNA from Escherichia coli acts as a versatile transcriptional regulator by binding to the RNA polymerase and changing promoter selectivity. Although homologous 6S RNA structures exist in a wide...read more

author A. Rediger, R. Geißen, B. Steuten, B. Heilmann, R. Wagner, I.M. Axmann
publication Microbiology
date 2012
download http://mic.sgmjournals.org/content/158/Pt_10/2480.long

Multi-Target Regulation by Small RNAs Synchronizes Gene Expression Thresholds and May Enhance Ultrasensitive Behavior.

Cells respond to external cues by precisely coordinating multiple molecular events. Co-regulation may be established by the so-called single-input module (SIM), where a common regulator controls...read more

author J.M. Schmiedel, I.M. Axmann, S.Legewie
publication PLoS One
date 2012
download http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0042296

The diversity of cyanobacterial metabolism: genome analysis of multiple phototrophic microorganisms

BACKGROUND: Cyanobacteria are among the most abundant organisms on Earth and represent one of the oldest and most widespread clades known in modern phylogenetics. As the only known...read more

author C. Beck, H. Knoop, I.M. Axmann, R.Steuer
publication BMC Genomics
date 2012
download http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3369817/

A sequestration feedback determines dynamics and temperature entrainment of the KaiABC circadian clock

The circadian rhythm of the cyanobacterium Synechococcus elongatus is controlled by three proteins, KaiA, KaiB, and KaiC. In a test tube, these proteins form complexes of various stoichiometry and...read more

author C. Brettschneider, R. J. Rose, S. Hertel, I. M. Axmann, A. J. R. Heck, M. Kollmann
publication Molecular Systems Biology
date 2010
download http://www.nature.com/msb/journal/v6/n1/synopsis/msb201044.html

Wie messen Bakterien die Zeit?

Die bislang einzigartige biochemische Uhr der Cyanobakterien lässt sich mit nur drei Proteinen und ATP im Reagenzglas nachbauen. Eine reduzierte Form dieses Systems zur Zeitmessung scheint hingegen...read more

author A. Wilde, I. M. Axmann
publication BioSpektrum
date Mai 2010
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Biochemical evidence for a timing mechanism in Prochlorococcus

Organisms coordinate biological activities into daily cycles using an internal circadian clock. The circadian oscillator proteins KaiA, KaiB and KaiC are widely believed to underlie 24-h oscillations...read more

author I. M. Axmann, U. Dühring, L. Seeliger, A. Arnold, J. T. Vanselow, A. Kramer, A. Wilde
publication Journal of  Bacteriology
date 2009
download http://jb.asm.org/cgi/content/full/191/17/5342?view=long&pmid=19502405

Small RNAs establish delays and temporal thresholds in gene expression

Organisms coordinate biological activities into daily cycles using an internal circadian clock. The circadian oscillator proteins KaiA, KaiB and KaiC are widely believed to underlie 24-h oscillations...read more

author S. Legewie, D. Dienst, A. Wilde, H. Herzel, I. M. Axmann
publication Biophysical Journal
date 2008
download http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2547459/?tool=pubmed

Two distinct types of 6S RNA in Prochlorococcus

Different forms of the 6S non-coding RNA (ncRNA) exist in enterobacteria and in B. subtilis but there is only limited information about this RNA from other groups of bacteria. Prochlorococcus is...read more

author I.M. Axmann, J. Holtzendorff, B. Voss, P. Kensche, W.R. Hess
publication Gene
date 2007
download http://www.sciencedirect.com

Genome-wide expression dynamics of a marine virus and host reveal features of co-evolution

Interactions between bacterial hosts and their viruses (phages) lead to reciprocal genome evolution through a dynamic co-evolutionary process. Phage-mediated transfer of host genes--often...read more

author D. Lindell, J.D. Jaffe, M.L. Coleman, M.E. Futschik, I.M. Axmann, T. Rector, G. Kettler, M.B. Sullivan, R. Steen, W.R. Hess, G.M. Church, S.W. Chisholm
publication Nature
date 2007
download http://www.nature.com/nature/journal/v449/n7158/full/nature06130.html

Regulatory elements of marine cyanobacteria

The free-living, oxyphototroph bacteria of the group of Prochlorococcus populate widely the oceans. Genomic information of nine marine cyanobacteria was used to predict signals essential for...read more

author S.M. Kiełbasa, H. Herzel, I.M. Axmann
publication Genome informatics. International Conference on Genome Informatics
date 2007
download https://www.jsbi.org/modules/journal1/index.php/IBSB07/IBSB07001.pdf

Functioning and robustness of a bacterial circadian clock

Cyanobacteria are the simplest known cellular systems that regulate their biological activities in daily cycles. For the cyanobacterium Synechococcus elongatus, it has been shown by in vitro and in...read more

author S. Clodong, U. Dühring, L. Kronk, A. Wilde, I.M. Axmann, H. Herzel, M. Kollmann
publication Molecular systems biology
date 2007
download http://www.nature.com/msb/journal/v3/n1/full/msb4100128.html

A motif-based search in bacterial genomes identifies the ortholog of the small RNA Yfr1 in all lineages of cyanobacteria

BACKGROUND: Non-coding RNAs (ncRNA) are regulators of gene expression in all domains of life. They control growth and differentiation, virulence, motility and various stress responses. The...read more

author B. Voss, G. Gierga, I.M. Axmann, W.R. Hess
publication BMC Genomics
date 2007
download http://www.biomedcentral.com/1471-2164/8/375

A minimal circadian clock model

  The coordination of biological activities into daily cycles provides an important advantage for the fitness of diverse organisms. Thereby, an internal circadian oscillator drives gene expression...read more

author I.M. Axmann,S. Legewie, H. Herzel
publication Genome informatics. International Conference on Genome Informatics
date 2007
download http://ebooks.worldscinet.com/ISBN/9781860949920/preserved-docs/9781860949920_0006.pdf

An internal antisense RNA regulates expression of the photosynthesis gene isiA

Small regulatory noncoding RNAs exist in both eukaryotic and prokaryotic organisms. Most of these RNA transcripts are trans-encoded RNAs with short and only partial antisense complementarity to...read more

author U. Dühring, I.M. Axmann, W.R. Hess, A. Wilde
publication Proceedings of the National Academy of Sciences of the United States of America
date 2006
download http://www.pnas.org/content/103/18/7054.full

Analyzing the Prochlorococcus light-harvesting system: regulatory sequence elements and novel antisera.

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author A. Rediger, I.M. Axmann, W.R. Hess
publication Photosynthesis: Fundamental Aspects to Global Perspectives, Proceedings 13 th International Congress on Photosynthesis
date 2005
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Identification of cyanobacterial non-coding RNAs by comparative genome analysis

BACKGROUND: Whole genome sequencing of marine cyanobacteria has revealed an unprecedented degree of genomic variation and streamlining. With a size of 1.66 megabase-pairs, Prochlorococcus sp. MED4...read more

author I.M. Axmann, P. Kensche, J. Vogel, S. Kohl, H. Herzel, W.R. Hess
publication Genome biology
date 2005
download http://genomebiology.com/2005/6/9/R73