Systems analyses characterize integrated functions of biochemical networks

Gianchandani, Erwin P.; Brautigan, David L.; Papin, Jason A.

doi:10.1016/j.tibs.2006.03.007

Cited by 30 publications

(24 citation statements)

References 63 publications

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“…For example, several transcription factors have been implicated in the inflammatory process associated with asthma, including the glucocorticoid receptor, NF-B, activator protein 1, nuclear factor of activated T-cells, cyclic AMP response element-binding protein, CEBP, PPAR, and NRF2 (38). Information on cross talk between signaling pathways may also provide insight into understanding the previously unrealized functions of a pathway and point to additional targets for interactions (11).…”

Section: Discussionmentioning

confidence: 99%

NRF2 Modulates Aryl Hydrocarbon Receptor Signaling: Influence on Adipogenesis

Shin¹,

Wakabayashi

Misra

et al. 2007

Molecular and Cellular Biology

295

216

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Section: Discussionmentioning

confidence: 99%

NRF2 Modulates Aryl Hydrocarbon Receptor Signaling: Influence on Adipogenesis

Shin¹,

Wakabayashi

Misra

et al. 2007

Molecular and Cellular Biology

295

216

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“…Structural analysis of PGAM5, by comparing with the recently reported crystal structure of Sts-1 (5), might reveal the molecular basis for substrate specificity exhibited by these unusual protein phosphatases. These discoveries of alternate activities will necessitate changing annotations of the PGAM family members in terms of their functions, which will alter integration of networks in systems biology (22).…”

Section: Conclusion and Perspectivementioning

confidence: 99%

Mitochondrial phosphoglycerate mutase 5 uses alternate catalytic activity as a protein serine/threonine phosphatase to activate ASK1

Takeda

Komuro

Hayakawa

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

129

133

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Phosphoglycerate mutase (PGAM) is an enzyme of intermediary metabolism that converts 3-phosphoglycerate to 2-phosphoglycerate in glycolysis. Here, we discovered PGAM5 that is anchored in the mitochondrial membrane lacks PGAM activity and instead associates with the MAP kinase kinase kinase ASK1 and acts as a specific protein Ser/Thr phosphatase that activates ASK1 by dephosphorylation of inhibitory sites. Mutation of an active site His-105 in PGAM5 abolished phosphatase activity with ASK1 and phospho-Thr peptides as substrates. The Drosophila and Caenorhabditis elegans orthologs of PGAM5 also exhibit specific Ser/Thr phosphatase activity and activate the corresponding Drosophila and C. elegans ASK1 kinases. PGAM5 is unrelated to the other known Ser/Thr phosphatases of the PPP, MPP, and FCP families, and our results suggest that this member of the PGAM family has crossed over from small molecules to protein substrates and been adapted to serve as a specialized activator of ASK1.MAP kinase ͉ protein phosphatase P hosphoglycerate mutase (PGAM) is an evolutionarily conserved enzyme of intermediary metabolism that converts 3-phosphoglycerate (3PG) to 2-phosphoglycerate (2PG) in glycolysis and the founder member of the PGAM protein family (1). Members of this family share a common catalytic domain, designated as the PGAM domain, and function as phosphotransferases and/or phosphohydrolases with small molecule substrates. For instance, 1,3-and 1,2-bisphosphoglycerate and fructose-2,6-bisphosphate are the substrates of well-characterized members of this family, the bisphosphoglycerate mutase (BPGM) and 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatases (PFKFB), respectively. The catalytic core of the PGAM domain centers on a histidine residue that acts as a phospho accepter during catalysis. These biochemical and structural features are also shared with the histidine acid phosphatase family of enzymes, and it has recently been proposed that these 2 families can be integrated into a histidine phosphatase superfamily (2). Whereas members of this superfamily predominantly target small molecule substrates, prostatic acid phosphatase has been shown to catalyze hydrolysis of high energy Phospho-Tyr bonds in substrates such as ErbB2 and EGF receptor (3, 4). In addition, Sts-1/TULA-2 in the PGAM family has been shown to function as a protein tyrosine phosphatase, dephosphorylating tyrosine kinases ZAP-70, Syk, and EGF receptor (5-7). These results open the possibility that enzymes in the PGAM family might regulate cellular functions beyond those in glucose metabolism.PGAM5 is a member of the PGAM family that has been shown to interact with Bcl-X L , an apoptosis regulator (8), and Keap1, a redox-regulated substrate adaptor for a cullindependent ubiquitin ligase complex (9). Although it has been suggested that the latter interaction is involved in the regulation of gene expression by the transcription factor Nrf2 (10), molecular functions of PGAM5 have not been elucidated. In this study, we identified PGAM5 as an interacting p...

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“…Although static biological systems have been well studied (Benfey & Mitchell-Olds, 2008;Gianchandani et al, 2006;Macilwain, 2011;Werner, 2007), the information gained from such studies is of limited use in moving forward due to the fact that the static interactions are often identified from cells exposed to a single condition or at a single time point, i.e., under nonnative conditions. Only recently have approaches emerged that attempt to analyze the dynamics of complex biological networks.…”

Section: Dynamic Networkmentioning

confidence: 99%

Comparative systems biology between human and animal models based on next-generation sequencing methods

Zhao

Li²,

Huang³

2013

Zoological Research

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Animal models provide myriad benefits to both experimental and clinical research. Unfortunately, in many situations, they fall short of expected results or provide contradictory results. In part, this can be the result of traditional molecular biological approaches that are relatively inefficient in elucidating underlying molecular mechanism. To improve the efficacy of animal models, a technological breakthrough is required. The growing availability and application of the high-throughput methods make systematic comparisons between human and animal models easier to perform. In the present study, we introduce the concept of the comparative systems biology, which we define as "comparisons of biological systems in different states or species used to achieve an integrated understanding of life forms with all their characteristic complexity of interactions at multiple levels". Furthermore, we discuss the applications of RNA-seq and ChIP-seq technologies to comparative systems biology between human and animal models and assess the potential applications for this approach in the future studies.

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Systems analyses characterize integrated functions of biochemical networks

Cited by 30 publications

References 63 publications

NRF2 Modulates Aryl Hydrocarbon Receptor Signaling: Influence on Adipogenesis

NRF2 Modulates Aryl Hydrocarbon Receptor Signaling: Influence on Adipogenesis

Mitochondrial phosphoglycerate mutase 5 uses alternate catalytic activity as a protein serine/threonine phosphatase to activate ASK1

Comparative systems biology between human and animal models based on next-generation sequencing methods

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