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Computational prediction of Pho regulons in cyanobacteria
Zhengchang Su, Victor Olman, Ying Xu
BMC Genomics , 2007, DOI: 10.1186/1471-2164-8-156
Abstract: We have predicted and analyzed the Pho regulons in 19 sequenced cyanobacterial genomes using a highly effective scanning algorithm that we have previously developed. Our results show that different cyanobacterial species/ecotypes may encode diverse sets of genes responsible for the utilization of various sources of phosphorus, ranging from inorganic phosphate, phosphodiester, to phosphonates. Unlike in E. coli, some cyanobacterial genes that are directly involved in phosphorus assimilation seem to not be under the regulation of the regulator SphR (orthologue of PhoB in E coli.) in some species/ecotypes. On the other hand, SphR binding sites are found for genes known to play important roles in other biological processes. These genes might serve as bridging points to coordinate the phosphorus assimilation and other biological processes. More interestingly, in three cyanobacterial genomes where no sphR gene is encoded, our results show that there is virtually no functional SphR binding site, suggesting that transcription regulators probably play an important role in retaining their binding sites.The Pho regulons in cyanobacteria are highly diversified to accommodate to their respective living environments. The phosphorus assimilation pathways in cyanobacteria are probably tightly coupled to a number of other important biological processes. The loss of a regulator may lead to the rapid loss of its binding sites in a genome.Cyanobacteria are among the oldest life form on Earth. These organisms inhabit a broad range of ecological environments from fresh water, soil to diverse open oceanographic areas [1]. It is estimated that several cyanobacteria living in the open oceans contribute a significant fraction of Earth's primary production [2]. These bacteria also play important roles in the global cycling of nitrogen and phosphorus [3,4]. Therefore their activities have significant impacts on global environmental changes.Phosphorus is one of the essential elements for all li
Selective inhibition of yeast regulons by daunorubicin: A transcriptome-wide analysis
Marta Rojas, Marta Casado, José Portugal, Benjamin Pi?a
BMC Genomics , 2008, DOI: 10.1186/1471-2164-9-358
Abstract: Daunorubicin affected a minor proportion (14%) of the yeast transcriptome, increasing the expression of 195 genes and reducing expression of 280 genes. Daunorubicin down-regulated genes included essentially all genes involved in the glycolytic pathway, the tricarboxylic acid cycle and alcohol metabolism, whereas transcription of ribosomal protein genes was not affected or even slightly increased. This pattern is consistent with a specific inhibition of glucose usage in treated cells, with only minor effects on proliferation or other basic cell functions. Analysis of promoters of down-regulated genes showed that they belong to a limited number of transcriptional regulatory units (regulons). Consistently, data mining showed that daunorubicin-induced changes in expression patterns were similar to those observed in yeast strains deleted for some transcription factors functionally related to the glycolysis and/or the cAMP regulatory pathway, which appeared to be particularly sensitive to daunorubicin.The effects of daunorubicin treatment on the yeast transcriptome are consistent with a model in which this drug impairs binding of different transcription factors by competing for their DNA binding sequences, therefore limiting their effectiveness and affecting the corresponding regulatory networks. This proposed mechanism might have broad therapeutic implications against cancer cells growing under hypoxic conditions.Understanding the mode of action of antitumor drugs is considered an absolute prerequisite for the advancement on the design of new drugs. It is generally believed that antitumor activity is mediated by the capacity of certain drugs to induce DNA damage and trigger apoptosis. However, there are many indications that this mechanism, whatever relevant may it be, does not account for all therapeutic effects of some antitumor drugs [1,2].The anthracycline antibiotic daunorubicin is widely used in cancer chemotherapy [3]. It accumulates in the nuclei of living cells
Computational biology and protein modeling of cyanobacteria using bioinformatics tools and techniques
Padhi S.B.,Behera S.,Swain P.,Behura S.
International Journal of Bioinformatics Research , 2010,
Abstract: Computational biology is a term coined from analogy to the role of physical sciences, is nowcoming into its own as a major element of contemporary biological and biomedical research. In the sharp inthis pattern, over past few years, experiments in life sciences in the academic institutions have begun torecognize the value of bioinformatics and computational biology in the field of algology. Cyanobacteria (alsoknown as blue–green algae) are a group of extraordinarily diverse Gram-negative prokaryotes thatoriginated 3.5 billion years ago. After the advent of bioinformatics in the field of algology, complete genomesequences of Cyanobacteria have been reported in more than 30 species and strains including unicellular.The filamentous cyanobacterium Anabaena sp. PCC 7120 (further referred to as Anabaena sp.) is a modelsystem to study nitrogen fixation, cell differentiation, cell pattern formation and evolution of plastids. It is amulticellular photosynthetic microorganism consisting of two cell types, vegetative cells and nitrogen fixingheterocysts. The nucleotide sequence of the entire genome of a filamentous Cyanobacterium, Anabaena sp.Strain PCC 7120, was determined. This study focuses on the function and dynamics of the proteome of theGram-negative outer membrane in Anabaena sp.
Genomic Arrangement of Regulons in Bacterial Genomes  [PDF]
Han Zhang, Yanbin Yin, Victor Olman, Ying Xu
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0029496
Abstract: Regulons, as groups of transcriptionally co-regulated operons, are the basic units of cellular response systems in bacterial cells. While the concept has been long and widely used in bacterial studies since it was first proposed in 1964, very little is known about how its component operons are arranged in a bacterial genome. We present a computational study to elucidate of the organizational principles of regulons in a bacterial genome, based on the experimentally validated regulons of E. coli and B. subtilis. Our results indicate that (1) genomic locations of transcriptional factors (TFs) are under stronger evolutionary constraints than those of the operons they regulate so changing a TF's genomic location will have larger impact to the bacterium than changing the genomic position of any of its target operons; (2) operons of regulons are generally not uniformly distributed in the genome but tend to form a few closely located clusters, which generally consist of genes working in the same metabolic pathways; and (3) the global arrangement of the component operons of all the regulons in a genome tends to minimize a simple scoring function, indicating that the global arrangement of regulons follows simple organizational principles.
The renaturation and activity study of LexA from Pseudomonas aeruginosa
铜绿假单胞菌SOS反应阻遏蛋白LexA的复性及活性研究

CHEN Xuan,TANG Shao-hui,CHA Qing-bing,TANG Hui,LIU Fang,
陈炫
,汤绍辉,查庆兵,唐晖,刘芳

中国生物工程杂志 , 2007,
Abstract: Objective To optimize the renaturation procedure of denatured LexA, prepare the repressor LexA from Pseudomonas aeruginosa (PA), which have the satisfactory biologic activity. Methods The LexA was renatured by the GSH/GSSG dilution method, and the renatured protein were purified by Ni2+ chelate affinity chromatography and gel filtration chromatography, following desalination by Sephadex G-25 gel column. The renaturation result were detected by the native polyacrylamide gel electrophoresis and RP-HPLC.The immunological activity of all LexA proteins, including the denatured , renatured protein and the renatured protein that was treated with the DTT, were determined by Western blot. Results The renatured LexA appears both monomer and multimer, which is confirmed by the native polyacrylamide gel electrophoresis analysis and RP-HPLC. Gel retardation experiments shows that the renatured LexA have satisfactory biologic activity.
PePPER: a webserver for prediction of prokaryote promoter elements and regulons
Anne de Jong, Hilco Pietersma, Martijn Cordes, Oscar P Kuipers, Jan Kok
BMC Genomics , 2012, DOI: 10.1186/1471-2164-13-299
Abstract: We here extend the current databases of TFs, TFBSs and regulons with our knowledge on Lactococcus lactis and developed a webserver for prediction, mining and visualization of prokaryote promoter elements and regulons via a novel concept. This new approach includes an all-in-one method of data mining for TFs, TFBSs, promoters, and regulons for any bacterial genome via a user-friendly webserver. We demonstrate the power of this method by mining WalRK regulons in Lactococci and Streptococci and, vice versa, use L. lactis regulon data (CodY) to mine closely related species.The PePPER webserver offers, besides the all-in-one analysis method, a toolbox for mining for regulons, promoters and TFBSs and accommodates a new L. lactis regulon database in addition to already existing regulon data. Identification of putative regulons and full annotation of intergenic regions in any bacterial genome on the basis of existing knowledge on a related organism can now be performed by biologists and it can be done for a wide range of regulons. On the basis of the PePPER output, biologist can design experiments to further verify the existence and extent of the proposed regulons. The PePPER webserver is freely accessible at http://pepper.molgenrug.nl webcite.
Genomewide Analysis of Carotenoid Cleavage Dioxygenases in Unicellular and Filamentous Cyanobacteria  [PDF]
Hongli Cui,Yinchu Wang,Song Qin
International Journal of Genomics , 2012, DOI: 10.1155/2012/164690
Abstract: Carotenoid cleavage dioxygenases (CCDs) are a group of enzymes that catalyze the oxidative cleavage steps from carotenoids to various carotenoid cleavage products. Some ccd genes have been identified and encoded enzymes functionally characterized in many higher plants, but little in cyanobacteria. We performed a comparative analysis of ccd sequences and explored their distribution, classification, phylogeny, evolution, and structure among 37 cyanobacteria. Totally 61 putative ccd sequences were identified, which are abundant in Acaryochloris marina MBIC 11017, filamentous N2-fixing cyanobacteria, and unicellular cyanobacterial Cyanothece. According to phylogenetic trees of 16S rDNA and CCD, nced and ccd8 genes occur later than the divergence of ccd7, apco, and ccd1. All CCD enzymes share conserved basic structure domains constituted by a single loop formed with seven β-strands and one helix. In this paper, a general framework of sequence-function-evolution connection for the ccd has been revealed, which may provide new insight for functional investigation. 1. Introduction Cyanobacteria, also known as blue-green algae and blue-green bacteria, are among the earliest branching groups on earth, dating back 2.5–3.5 billion years, based on the fossil evidence [1]. They may be unicellular or filamentous and can be found in almost every conceivable environment, such as marine and freshwater habitats, soil, rocks, and plants [2, 3]. With the capacity of oxygenic photosynthesis similar to the process found in higher plants, cyanobacteria constitute a group of species diverse not only in ecological habitat, but also in genome size and the number of gene, indicating the significance of comparative genome research. The genome size varied from 1.6?Mb (Prochlorococcus sp. MIT9301) to 9.0?Mb (Nostoc punctiforme PCC 73102), and the number of gene ranged from 1,756 (Prochlorococcus marinus MED4) to 8,462 (Acaryochloris marina MBIC11017) [4–6]. A lot of information on the evolutionary history of cyanobacteria has strongly supported an underlying meaning of comparative genome research. Three major clades are observed in cyanobacteria phylogenetic tree (Figure 1). The unicellular cyanobacteria (Prochlorococcus and Synechococcus) from ocean form the first monophyletic group (BS: 98%). They maintain the smallest genome size and account for significant biomass and primary production of marine biosphere [7]. Two Synechococcus elongatus PCC (6301 and 7942) are found at the base of this monophyletic group. Three thermophilic cyanobacteria (Synechococcus sp. JA-2-3B′a (2-13),
Genomewide Analysis of Carotenoid Cleavage Dioxygenases in Unicellular and Filamentous Cyanobacteria  [PDF]
Hongli Cui,Yinchu Wang,Song Qin
Comparative and Functional Genomics , 2012, DOI: 10.1155/2012/164690
Abstract: Carotenoid cleavage dioxygenases (CCDs) are a group of enzymes that catalyze the oxidative cleavage steps from carotenoids to various carotenoid cleavage products. Some ccd genes have been identified and encoded enzymes functionally characterized in many higher plants, but little in cyanobacteria. We performed a comparative analysis of ccd sequences and explored their distribution, classification, phylogeny, evolution, and structure among 37 cyanobacteria. Totally 61 putative ccd sequences were identified, which are abundant in Acaryochloris marina MBIC 11017, filamentous N2-fixing cyanobacteria, and unicellular cyanobacterial Cyanothece. According to phylogenetic trees of 16S rDNA and CCD, nced and ccd8 genes occur later than the divergence of ccd7, apco, and ccd1. All CCD enzymes share conserved basic structure domains constituted by a single loop formed with seven β-strands and one helix. In this paper, a general framework of sequence-function-evolution connection for the ccd has been revealed, which may provide new insight for functional investigation.
Listeria monocytogenes Differential Transcriptome Analysis Reveals Temperature-Dependent Agr Regulation and Suggests Overlaps with Other Regulons  [PDF]
Dominique Garmyn, Yoann Augagneur, Laurent Gal, Anne-Laure Vivant, Pascal Piveteau
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0043154
Abstract: Listeria monocytogenes is a ubiquitous, opportunistic pathogenic organism. Environmental adaptation requires constant regulation of gene expression. Among transcriptional regulators, AgrA is part of an auto-induction system. Temperature is an environmental cue critical for in vivo adaptation. In order to investigate how temperature may affect AgrA-dependent transcription, we compared the transcriptomes of the parental strain L. monocytogenes EGD-e and its ΔagrA mutant at the saprophytic temperature of 25°C and in vivo temperature of 37°C. Variations of transcriptome were higher at 37°C than at 25°C. Results suggested that AgrA may be involved in the regulation of nitrogen transport, amino acids, purine and pyrimidine biosynthetic pathways and phage-related functions. Deregulations resulted in a growth advantage at 37°C, but affected salt tolerance. Finally, our results suggest overlaps with PrfA, σB, σH and CodY regulons. These overlaps may suggest that through AgrA, Listeria monocytogenes integrates information on its biotic environment.
Transcriptome analysis of differentiating trypanosomes reveals the existence of multiple post-transcriptional regulons
Rafael Queiroz, Corinna Benz, Kurt Fellenberg, J?rg D Hoheisel, Christine Clayton
BMC Genomics , 2009, DOI: 10.1186/1471-2164-10-495
Abstract: Some mRNAs showed changes within 30 min of cis-aconitate addition, whereas others responded 12-24 hours later. For the first 12 h after addition of cis-aconitate, cells accumulated at the G1 phase of the cell cycle, and showed decreases in mRNAs required for proliferation, mimicking the changes seen in stumpy forms: many mRNAs needed for ribosomal and flagellar biogenesis showed striking co-regulation. Other mRNAs encoding components of signal transduction pathways and potential regulators were specifically induced only during differentiation. Messenger RNAs encoding proteins required for individual metabolic pathways were often co-regulated.Trypanosome genes form post-transcriptional regulons in which mRNAs with functions in particular pathways, or encoding components of protein complexes, show almost identical patterns of regulation.African trypanosomes grow in various mammalian hosts and in Tsetse flies, and are extracellular throughout their life cycle. Within the mammal, the cells grow as long slender trypomastigotes in the blood and tissue fluids, depending on glucose and substrate-level phosphorylation for ATP generation and having a very poorly developed mitochondrion. The bloodstream-form trypanosomes are coated with Variant Surface Glycoprotein (VSG), which is anchored to the plasma membrane by glycosyl phosphatidylinositol; a combination of genetic rearrangements and transcriptional switching of the VSG expressed enables indefinite evasion of humoral immunity. As the parasitaemia increases, a mechanism resembling quorum sensing [1-3] allows some cells to take on a "stumpy" morphology. Stumpy bloodstream-form trypanosomes are arrested in the G1 phase of the cell cycle, and express some mitochondrial proteins that are not detected in the long slender forms [4].Differentiation of bloodstream forms into procyclic forms, which multiply in the midgut of the Tsetse fly (reviewed in [5]), can be triggered by various stimuli, including addition of cis-aconitate [6
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