Functional Genomics and Systems Biology Group

Schönau am Königssee, Germany

Functional Genomics and Systems Biology Group

Schönau am Königssee, Germany

Time filter

Source Type

Naseem M.,Functional Genomics and Systems Biology Group | Kunz M.,Functional Genomics and Systems Biology Group | Ahmed N.,University for Information Science and Technology | Dandekar T.,Functional Genomics and Systems Biology Group
Plant Signaling and Behavior | Year: 2013

Crosstalk between auxin and cytokinin in plant growth and development has already been established. However, their dynamics in plant immunity is still not well understood and requires systems biological approaches for analysis. Omics based public databases are exploited for the reconstruction, integration and analysis of Boolean models for hormonal interactions in plants. We established a meta-network by combining the plant immune regulatory network and the pathogen virulence specific network and used it as substrate for dynamic simulations on hormonal aspects of plant immunity. Our integrated analysis of this meta-network reveals antagonistic crosstalk between auxin and cytokinin in the Pst DC3000 and Arabidopsis interaction. Moreover, we discuss here the importance of Boolean models in unfolding inferences relevant to plant pathogen interactions. © 2013 Landes Bioscience.


Naseem M.,Functional Genomics and Systems Biology Group | Kaltdorf M.,Functional Genomics and Systems Biology Group | Dandekar T.,Functional Genomics and Systems Biology Group
Journal of Experimental Botany | Year: 2015

Plants deploy a finely tuned balance between growth and defence responses for better fitness. Crosstalk between defence signalling hormones such as salicylic acid (SA) and jasmonates (JAs) as well as growth regulators plays a significant role in mediating the trade-off between growth and defence in plants. Here, we specifically discuss how the mutual antagonism between the signalling of auxin and SA impacts on plant growth and defence. Furthermore, the synergism between auxin and JA benefits a class of plant pathogens. JA signalling also poses growth cuts through auxin. We discuss how the effect of cytokinins (CKs) is multifaceted and is effective against a broad range of pathogens in mediating immunity. The synergism between CKs and SA promotes defence against biotrophs. Reciprocally, SA inhibits CK-mediated growth responses. Recent reports show that CKs promote JA responses; however, in a feedback loop, JA suppresses CK responses. We also highlight crosstalk between auxin and CKs and discuss their antagonistic effects on plant immunity. Efforts to minimize the negative effects of auxin on immunity and a reduction in SA- and JA-mediated growth losses should lead to better sustainable plant protection strategies. © 2015 The Author 2015. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved.


Naseem M.,Functional Genomics and Systems Biology group | Kaltdorf M.,Functional Genomics and Systems Biology group | Hussain A.,Abdul Wali Khan University Mardan | Dandekar T.,Functional Genomics and Systems Biology group
Plant Signaling and Behavior | Year: 2013

Cytokinin has long been shown to be an essential modulator of growth and development in plants. However, its implications in plant immunity have only recently been realized. The interaction between jasmonate and salicylate pathways is regarded as a central backbone of plant immune defense. However, the effect of cytokinin on the jasmonate and salicylate mediated balance in plant immunity is still not known. Here, we analyze the impact of cytokinin on the jasmonate-salicylate antagonism in Arabidopsis immunity regarding infection with hemibiotrophic pathogen Pseudomonas syringae pv tomato DC3000 (Pst DC3000). Systems biology analysis of a refined hormone immune pathway model provides insights into the impact of cytokinin on the balance between jasmonate and salicylic acid pathways in Arabidopsis. Targeted experiments validate model simulations monitoring bacterial growth in wild type plants as well as in jasmonate pathway mutants. An integrated analysis shows that CK promotes the SA pathway of plant immunity and does not promote JA-mediated Arabidopsis susceptibility against infection with Pst DC3000. Finally, we discuss these results in the context of an emerging model of auxin-cytokinin antagonism in plant immunity. © 2013 Landes Bioscience.


Naseem M.,Functional Genomics and Systems Biology group | Srivastava M.,Functional Genomics and Systems Biology group | Tehseen M.,King Abdullah University of Science and Technology | Ahmed N.,University of Balochistan
Current Protein and Peptide Science | Year: 2015

The plant hormone auxin regulates a whole repertoire of plant growth and development. Many plant-associated microorganisms, by virtue of their auxin production capability, mediate phytostimulation effects on plants. Recent studies, however, demonstrate diverse mechanisms whereby plant pathogens manipulate auxin biosynthesis, signaling and transport pathways to promote host susceptibility. Auxin responses have been coupled to their antagonistic and synergistic interactions with salicylic acid and jasmonate mediated defenses, respectively. Here, we discuss that a better understanding of auxin crosstalk to plant immune networks would enable us to engineer crop plants with higher protection and low unintended yield losses. © 2015 Bentham Science Publishers.


Naseem M.,Functional Genomics and Systems Biology Group
Plant signaling & behavior | Year: 2013

Crosstalk between auxin and cytokinin in plant growth and development has already been established. However, their dynamics in plant immunity is still not well understood and requires systems biological approaches for analysis. Omics based public databases are exploited for the reconstruction, integration and analysis of Boolean models for hormonal interactions in plants. We established a meta-network by combining the plant immune regulatory network and the pathogen virulence specific network and used it as substrate for dynamic simulations on hormonal aspects of plant immunity. Our integrated analysis of this meta-network reveals antagonistic crosstalk between auxin and cytokinin in the Pst DC3000 and Arabidopsis interaction. Moreover, we discuss here the importance of Boolean models in unfolding inferences relevant to plant pathogen interactions.


Naseem M.,Functional Genomics and Systems Biology Group | Kunz M.,Functional Genomics and Systems Biology Group | Dandekar T.,Functional Genomics and Systems Biology Group
Bioinformatics and Biology Insights | Year: 2014

Plant hormones involving salicylic acid (SA), jasmonic acid (JA), ethylene (Et), and auxin, gibberellins, and abscisic acid (ABA) are known to regulate host immune responses. However, plant hormone cytokinin has the potential to modulate defense signaling including SA and JA. It promotes plant pathogen and herbivore resistance; underlying mechanisms are still unknown. Using systems biology approaches, we unravel hub points of immune interaction mediated by cytokinin signaling in Arabidopsis. High-confidence Arabidopsis protein-protein interactions (PPI) are coupled to changes in cytokinin-mediated gene expression. Nodes of the cellular interactome that are enriched in immune functions also reconstitute sub-networks. Topological analyses and their specific immunological relevance lead to the identification of functional hubs in cellular interactome. We discuss our identified immune hubs in light of an emerging model of cytokinin-mediated immune defense against pathogen infection in plants. © the authors, publisher and licensee Libertas Academica Limited.


Kaltdorf M.,Functional Genomics and Systems Biology Group | Naseem M.,Functional Genomics and Systems Biology Group
Science Signaling | Year: 2013

The small-molecule hormone salicylic acid (SA) is a plant immune signal for which the receptors have only recently been identifi ed. Two recent studies reported that the transcriptional coactivator nonexpresser of pathogenesis-related genes 1 (NPR1) and its paralogues NPR3 and NPR4 are bona fi de SA immune signal receptors in plants. Fu et al. demonstrated that because of their binding affinity for SA, NPR3 and NPR4 are SA receptors for immune responses in Arabidopsis thaliana. Both NPR3 and NPR4 function as adaptors in proteasomal degradation of NPR1 in an SA-dependent manner. By applying nonequilibrium methods, they showed very low binding affi nity of NPR1 for SA, suggesting that it may not qualify as an SA immune signal transduction receptor. However, using a method of equilibrium dialysis, Wu et al. found that SA binds to NPR1 and induces a conformational change in NPR1 or introduces steric hindrance that relieves repression of the transcriptional activation domain of NPR1 by an autoinhibitory N-terminal domain. This derepression leads to the expression of SA-dependent defense genes. Here, we discuss the importance of emerging SA perception models.


PubMed | Functional Genomics and Systems Biology Group
Type: Journal Article | Journal: Journal of experimental botany | Year: 2015

Plants deploy a finely tuned balance between growth and defence responses for better fitness. Crosstalk between defence signalling hormones such as salicylic acid (SA) and jasmonates (JAs) as well as growth regulators plays a significant role in mediating the trade-off between growth and defence in plants. Here, we specifically discuss how the mutual antagonism between the signalling of auxin and SA impacts on plant growth and defence. Furthermore, the synergism between auxin and JA benefits a class of plant pathogens. JA signalling also poses growth cuts through auxin. We discuss how the effect of cytokinins (CKs) is multifaceted and is effective against a broad range of pathogens in mediating immunity. The synergism between CKs and SA promotes defence against biotrophs. Reciprocally, SA inhibits CK-mediated growth responses. Recent reports show that CKs promote JA responses; however, in a feedback loop, JA suppresses CK responses. We also highlight crosstalk between auxin and CKs and discuss their antagonistic effects on plant immunity. Efforts to minimize the negative effects of auxin on immunity and a reduction in SA- and JA-mediated growth losses should lead to better sustainable plant protection strategies.


PubMed | Functional Genomics and Systems Biology Group
Type: | Journal: Bioinformatics and biology insights | Year: 2014

Plant hormones involving salicylic acid (SA), jasmonic acid (JA), ethylene (Et), and auxin, gibberellins, and abscisic acid (ABA) are known to regulate host immune responses. However, plant hormone cytokinin has the potential to modulate defense signaling including SA and JA. It promotes plant pathogen and herbivore resistance; underlying mechanisms are still unknown. Using systems biology approaches, we unravel hub points of immune interaction mediated by cytokinin signaling in Arabidopsis. High-confidence Arabidopsis protein-protein interactions (PPI) are coupled to changes in cytokinin-mediated gene expression. Nodes of the cellular interactome that are enriched in immune functions also reconstitute sub-networks. Topological analyses and their specific immunological relevance lead to the identification of functional hubs in cellular interactome. We discuss our identified immune hubs in light of an emerging model of cytokinin-mediated immune defense against pathogen infection in plants.


PubMed | Functional Genomics and Systems Biology Group, Hannover Medical School, University of Würzburg and Imperial College London
Type: Journal Article | Journal: Journal of molecular and cellular cardiology | Year: 2015

MicroRNAs (miRNAs) are small ~22 nucleotide non-coding RNAs and are highly conserved among species. Moreover, miRNAs regulate gene expression of a large number of genes associated with important biological functions and signaling pathways. Recently, several miRNAs have been found to be associated with cardiovascular diseases. Thus, investigating the complex regulatory effect of miRNAs may lead to a better understanding of their functional role in the heart. To achieve this, bioinformatics approaches have to be coupled with validation and screening experiments to understand the complex interactions of miRNAs with the genome. This will boost the subsequent development of diagnostic markers and our understanding of the physiological and therapeutic role of miRNAs in cardiac remodeling. In this review, we focus on and explain different bioinformatics strategies and algorithms for the identification and analysis of miRNAs and their regulatory elements to better understand cardiac miRNA biology. Starting with the biogenesis of miRNAs, we present approaches such as LocARNA and miRBase for combining sequence and structure analysis including phylogenetic comparisons as well as detailed analysis of RNA folding patterns, functional target prediction, signaling pathway as well as functional analysis. We also show how far bioinformatics helps to tackle the unprecedented level of complexity and systemic effects by miRNA, underlining the strong therapeutic potential of miRNA and miRNA target structures in cardiovascular disease. In addition, we discuss drawbacks and limitations of bioinformatics algorithms and the necessity of experimental approaches for miRNA target identification. This article is part of a Special Issue entitled Non-coding RNAs.

Loading Functional Genomics and Systems Biology Group collaborators
Loading Functional Genomics and Systems Biology Group collaborators