The Unique Cyanobacterial Protein OpcA Is an Allosteric Effector of Glucose-6-phosphate Dehydrogenase in Nostoc punctiformeATCC 29133

Hagen, Kari D.; Meeks, John C.

doi:10.1074/jbc.m010472200

Cited by 55 publications

(53 citation statements)

References 26 publications

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“…OpcA has been shown to acts as an allosteric activator of Glucose-6-Phosphate dehydrogenase (G6PD) in Nostoc punctiforme, which is an essential enzyme for nitrogen fixation and dark heterotrophic growth. 12 Being OpcA an allosteric activator, it could be hypothesized that OpcA also activates the molecule responsible of proliferating HIP1. However, a spurious association between OpcA and HIP1 abundance can't be ruled out.…”

Section: Discussionmentioning

confidence: 99%

Abundance and distribution of the highly iterated palindrome 1 (HIP1) among prokaryotes

Delaye

Moya

2011

Mobile Genetic Elements

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Abbreviations: HIP1, highly iterated palindrome 1; HGT, horizontal gene transfer; SDR, small dispersed repeat;OpcA, glucose 6-phosphate dehydrogenase assembly proteinWe have studied the abundance and phylogenetic distribution of the Highly Iterated Palindrome 1 (HIP1) among sequenced prokaryotic genomes. We show that an overrepresentation of HIP1 is exclusive of some lineages of cyanobacteria, and that this abundance was gained only once during evolution and was subsequently lost in the lineage leading to marine pico-cyanobacteria. We show that among cyanobacterial protein sequences with annotated Pfam domains, only OpcA (glucose 6-phosphate dehydrogenase assembly protein) has a phylogenetic distribution fully matching HIP1 abundance, suggesting a functional relationship; we also show that DAM methylase (an enzyme that has the four central nucleotides of HIP1 as is site of action) is present in all cyanobacterial genomes (independently of their HIP1 content) with the exception of marine pico-cyanobacteria whom might have lost this enzyme during the process of genome reduction. Our analyses also show that in some prokaryotic lineages (particularly in those species with large genomes), HIP1 is unevenly distributed between coding and non-coding DNA (being more common in coding regions; with the exception of Cyanobacteria Yellowstone B' and Synechococcus elongates where the reverse pattern is true). Finally, we explore the hypothesis that the HIP1 can be used as a molecular "water-mark" to identify horizontally transferred genes from cyanobacteria to other species.

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Section: Discussionmentioning

confidence: 99%

Abundance and distribution of the highly iterated palindrome 1 (HIP1) among prokaryotes

Delaye

Moya

2011

Mobile Genetic Elements

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“…1). The oxidative pentose phosphate (OPP) pathway enzyme 6-phosphogluconate dehydrogenase (6PGD, Sp25) was highly abundant, while glucose-6-phosphate dehydrogenase (G6PD) (Summers et al, 1995;Hagen & Meeks, 2001) was not identified. The latter finding corroborates earlier data showing that light inhibits the activity of G6PD in Anabaena sp.…”

Section: Discussionmentioning

confidence: 99%

Proteomic analyses of the photoauto- and diazotrophically grown cyanobacterium Nostoc sp. PCC 73102

et al. 2007

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The filamentous cyanobacteria of the genus Nostoc are globally distributed, phenotypically complex organisms, capable of cellular differentiation and of forming symbiotic associations with a wide range of plants. To further our understanding of these processes and functions, the proteome of photoautotrophically and diazotrophically grown Nostoc sp. PCC 73102 (N. punctiforme) cells was examined. Extracted proteins were separated into membrane and soluble protein fractions and analysed using two-dimensional gel electrophoresis and matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS). The analysis led to the identification of 82 proteins that could be divided into 12 functional categories. Significantly, 65 of these proteins have not been previously documented in the Nostoc proteome. Many of the proteins identified were readily recognized as housekeeping proteins involved in carbon, nitrogen and energy metabolism, but a number of proteins related to stress, motility, secretion and post-translational modifications were also identified. Ten unclassified proteins were also detected, representing potential novel functions. These proteins were highly expressed, suggesting that they play key roles during photoautotrophic and diazotrophic growth. Nineteen of the proteins expressed under the growth conditions examined contained putative thioredoxin (Trx) targets, a motif that functions in redox regulation via redox equivalent mediators and is known to be significant in a wide range of biological processes. These observations contribute to our understanding of the complex Nostoc life cycle.

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“…7A) (Supplementary file S6), including OpcA, the unique cyanobacterial Zwf activator (Hagen and Meeks 2001). In contrast, only two of the 6 KGs listed for NADP(H)-metabolism were retained by the script (Fig.…”

Section: Case Study 2 -Nadp(h)-metabolismmentioning

confidence: 99%

“…PCC 7424, and links to Zwf via slr1793 (talu) and slr1734. The latter gene is a homolog of OpcA, an allosteric regulator and activation factor of Zwf in other cyanobacteria (Hagen and Meeks 2001).…”

Section: Case Study 2 -Nadp(h)-metabolismmentioning

confidence: 99%

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Finding novel relationships with integrated gene-gene association network analysis of Synechocystis sp. PCC 6803 using species-independent text-mining

Kreula

Kaewphan

Ginter

et al. 2017

Preprint

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The increasing move towards open access full-text scientific literature enhances our ability to utilize advanced text-mining methods to construct information-rich networks that no human will be able to grasp simply from 'reading the literature'. The utility of text-mining for well-studied species is obvious though the utility for less studied species, or those with no prior track-record at all, is not clear. Here we present a concept for how advanced textmining can be used to create information-rich networks even for less well studied species and apply it to generate an open-access gene-gene association network resource for Synechocystis sp. PCC 6803, a representative model organism for cyanobacteria and first case-study for the methodology. By merging the text-mining network with networks generated from species-specific experimental data, network integration was used to enhance the accuracy of predicting novel interactions that are biologically relevant. A rulebased algorithm was constructed in order to automate the search for novel candidate genes with a high degree of likely association to known target genes by (1) ignoring established relationships from the existing literature, as they are already 'known', and (2) demanding multiple independent evidences for every novel and potentially relevant relationship. Using selected case studies, we demonstrate the utility of the network resource and rule-based algorithm to (i) discover novel candidate associations between different genes or proteins in the network, and (ii) rapidly evaluate the potential role of ABSTRACTThe increasing move towards open access full-text scientific literature enhances our ability to utilize advanced text-mining methods to construct information-rich networks that no human will be able to grasp simply from 'reading the literature'. The utility of text-mining for well-studied species is obvious though the utility for less studied species, or those with no prior track-record at all, is not clear. Here we present a concept for how advanced text-mining can be used to create information-rich networks even for less well studied species and apply it to generate an openaccess gene-gene association network resource for Synechocystis sp. PCC 6803, a representative model organism for cyanobacteria and first case-study for the methodology. uy merging the textmining network with networks generated from species-specific experimental data, network integration was used to enhance the accuracy of predicting novel interactions that are biologically relevant. A rule-based algorithm was constructed in order to automate the search for novel candidate genes with a high degree of likely association to known target genes by (1) ignoring established relationships from the existing literature, as they are already 'known', and (2) demanding multiple independent evidences for every novel and potentially relevant relationship. Using selected case studies, we demonstrate the utility of the network resource and rule-based algorithm to (i) discover novel candidate ass...

show abstract

The Unique Cyanobacterial Protein OpcA Is an Allosteric Effector of Glucose-6-phosphate Dehydrogenase in Nostoc punctiformeATCC 29133

Cited by 55 publications

References 26 publications

Abundance and distribution of the highly iterated palindrome 1 (HIP1) among prokaryotes

Abundance and distribution of the highly iterated palindrome 1 (HIP1) among prokaryotes

Proteomic analyses of the photoauto- and diazotrophically grown cyanobacterium Nostoc sp. PCC 73102

Finding novel relationships with integrated gene-gene association network analysis of Synechocystis sp. PCC 6803 using species-independent text-mining

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