The Rhodobacter sphaeroides 2.4.1 rho gene: expression and genetic analysis of structure and function.

To understand the commitment of the genome to nervous system differentiation and function, we sought to compare nervous system gene expression to that of a wide variety of other tissues by gene expression database construction and mining. Gene expression profiles of 10 different adult nervous tissues were compared with that of 72 other tissues. Using ANOVA, we identified 1,361 genes whose expression was higher in the nervous system than other organs and, separately, 600 genes whose expression was at least threefold higher in one or more regions of the nervous system compared with their median expression across all organs. Of the 600 genes, 381 overlapped with the 1,361-gene list. Limited in situ gene expression analysis confirmed that identified genes did represent nervous system-enriched gene expression, and we therefore sought to evaluate the validity and significance of these top-ranked nervous system genes using known gene literature and gene ontology categorization criteria. Diverse functional categories were present in the 381 genes, including genes involved in intracellular signaling, cytoskeleton structure and function, enzymes, RNA metabolism and transcription, membrane proteins, as well as cell differentiation, death, proliferation, and division. We searched existing public sites and identified 110 known genes related to mental retardation, neurological disease, and neurodegeneration. Twenty-one of the 381 genes were within the 110-gene list, compared with a random expectation of 5. This suggests that the 381 genes provide a candidate set for further analyses in neurological and psychiatric disease studies and that as a field, we are as yet, far from a large-scale understanding of the genes that are critical for nervous system structure and function. Together, our data indicate the power of profiling an individual biologic system in a multisystem context to gain insight into the genomic basis of its structure and function.

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The essential activities of the bacterial sigma factor

Canadian Journal of Microbiology ◽

10.1139/cjm-2016-0576 ◽

2017 ◽

Vol 63 (2) ◽

pp. 89-99 ◽

Cited By ~ 16

Author(s):

Maria C. Davis ◽

Christopher A. Kesthely ◽

Emily A. Franklin ◽

Shawn R. MacLellan

Keyword(s):

Gene Expression ◽

Transcription Factors ◽

Rna Synthesis ◽

Gene Expression Regulation ◽

Structure And Function ◽

Structural Studies ◽

General Transcription Factors ◽

Transcription Process ◽

Promoter Dna ◽

And Function

Transcription is the first and most heavily regulated step in gene expression. Sigma (σ) factors are general transcription factors that reversibly bind RNA polymerase (RNAP) and mediate transcription of all genes in bacteria. σ Factors play 3 major roles in the RNA synthesis initiation process: they (i) target RNAP holoenzyme to specific promoters, (ii) melt a region of double-stranded promoter DNA and stabilize it as a single-stranded open complex, and (iii) interact with other DNA-binding transcription factors to contribute complexity to gene expression regulation schemes. Recent structural studies have demonstrated that when σ factors bind promoter DNA, they capture 1 or more nucleotides that are flipped out of the helical DNA stack and this stabilizes the promoter open-complex intermediate that is required for the initiation of RNA synthesis. This review describes the structure and function of the σ70 family of σ proteins and the essential roles they play in the transcription process.

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Structure and Function of the Photosynthetic Reaction Center of Rhodobacter sphaeroides

Photosynthetic Reaction Center ◽

10.1016/b978-0-12-208661-8.50006-1 ◽

1993 ◽

pp. 1-12

Author(s):

Marianne Schiffer ◽

James R. Norris

Keyword(s):

Reaction Center ◽

Rhodobacter Sphaeroides ◽

Photosynthetic Reaction Center ◽

Structure And Function ◽

And Function

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mirror, a Drosophila homeobox gene in the Iroquois complex, is required for sensory organ and alula formation

Development ◽

10.1242/dev.125.7.1217 ◽

1998 ◽

Vol 125 (7) ◽

pp. 1217-1227 ◽

Cited By ~ 2

Author(s):

B.T. Kehl ◽

K.O. Cho ◽

K.W. Choi

Keyword(s):

Protein Structure ◽

Genetic Analysis ◽

Genetic Map ◽

Body Wall ◽

Homeobox Gene ◽

Structure And Function ◽

The Other ◽

Complex Region ◽

Sensory Bristles ◽

And Function

The Drosophila notum, the dorsal body wall of the thorax, is subdivided genetically into longitudinal domains (Calleja, M., Moreno, E., Pelaz, S. and Morata, G. (1996) Science 274, 252–255). Two homeobox genes clustered in the iroquois complex, araucan and caupolican, regulate proneural genes and are required for development of sensory bristles in the lateral notum (Gomez-Skarmeta, J. L., del Corral, R. D., de la Calle-Mustienes, E., Ferres-Marco, D. and Modolell, J. (1996) Cell 85, 95–105). An iroquois-related homeobox gene, mirror, was recently isolated and is localized close to the iroquois complex region (McNeil, H., Yang, C.-H., Brodsky, M., Ungos, J. and Simon, M. A. (1997) Genes and Development 11, 1073–1082; this study). We show that mirror is required for the formation of the alula and a subset of sensory bristles in the lateral domain of the notum. Genetic analysis suggests that mirror and the other iroquois genes interact to form the alula as well as the sensory organs. Based on similarities between mirror and the iroquois genes in their genetic map positions, expression, protein structure and function, mirror is considered a new member of the iroquois complex and is involved in prepatterning sensory precursor cells in the lateral notum.

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Renal ischemia alters expression of mitochondria-related genes and impairs mitochondrial structure and function in swine scattered tubular-like cells

AJP Renal Physiology ◽

10.1152/ajprenal.00120.2020 ◽

2020 ◽

Vol 319 (1) ◽

pp. F19-F28 ◽

Cited By ~ 1

Author(s):

Rahele A. Farahani ◽

Xiang-Yang Zhu ◽

Hui Tang ◽

Kyra L. Jordan ◽

Lilach O. Lerman ◽

...

Keyword(s):

Gene Expression ◽

Structural Damage ◽

Nuclear Dna ◽

Mitochondrial Genes ◽

Structure And Function ◽

Mitochondrial Damage ◽

Renal Ischemia ◽

Gene Gain ◽

Mitochondrial Structure ◽

And Function

Scattered tubular-like cells (STCs) are dedifferentiated surviving tubular epithelial cells that repair neighboring injured cells. Experimental renal artery stenosis (RAS) impairs STC reparative potency by inducing mitochondrial injury, but the exact mechanisms of mitochondrial damage remain unknown. We hypothesized that RAS alters expression of mitochondria-related genes, contributing to mitochondrial structural damage and dysfunction in swine STCs. CD24+/CD133+ STCs were isolated from pig kidneys after 10 wk of RAS or sham ( n = 3 each). mRNA sequencing was performed, and nuclear DNA (nDNA)-encoded mitochondrial genes and mitochondrial DNA (mtDNA)-encoded genes were identified. Mitochondrial structure, ATP generation, biogenesis, and expression of mitochondria-associated microRNAs were also assessed. There were 96 nDNA-encoded mitochondrial genes upregulated and 12 mtDNA-encoded genes downregulated in RAS-STCs versus normal STCs. Functional analysis revealed that nDNA-encoded and mtDNA-encoded differentially expressed genes were primarily implicated in mitochondrial respiration and ATP synthesis. Mitochondria from RAS STCs were swollen and showed cristae remodeling and loss and decreased ATP production. Immunoreactivity of the mitochondrial biogenesis marker peroxisome proliferator-activated receptor-γ coactivator (PGC)-1α and expression of the mitochondria-associated microRNAs miR-15a, miR-181a, miR-196a, and miR-296-3p, which target several mtDNA genes, were higher in RAS-STCs compared with normal STCs, suggesting a potential modulation of mitochondria-related gene expression. These results demonstrate that RAS induces an imbalance in mtDNA- and nDNA-mitochondrial gene expression, impairing mitochondrial structure and function in swine STCs. These observations support development of gene gain- and loss-of-function strategies to ameliorate mitochondrial damage and preserve the reparative potency of STCs in patients with renal ischemia.

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Genetic analysis of the structure and function of RNase P fromE. coli

Molecular Biology Reports ◽

10.1007/bf00988714 ◽

1996 ◽

Vol 22 (2-3) ◽

pp. 111-114

Author(s):

Hideaki Shiraishi ◽

Yoshiro Shimura

Keyword(s):

Genetic Analysis ◽

Rnase P ◽

Structure And Function ◽

And Function

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Frank William Ernest Gibson 1923 - 2008

Historical Records of Australian Science ◽

10.1071/hr09024 ◽

2010 ◽

Vol 21 (1) ◽

pp. 55 ◽

Cited By ~ 1

Author(s):

A. J. Pittard ◽

G. B. Cox

Keyword(s):

Escherichia Coli ◽

Amino Acids ◽

Genetic Analysis ◽

Aromatic Compounds ◽

Aromatic Amino Acids ◽

Atp Synthesis ◽

Structure And Function ◽

Innovative Model ◽

Distinguished Research ◽

And Function

Frank Gibson died in Canberra on 11 July 2008. Frank was a highly distinguished research scientist who will be remembered for his pioneering studies in identifying the branch-point compound in the pathway of biosynthesis of a large number of important aromatic compounds followed by a detailed biochemical and genetic analysis of many of the pathways leading to the aromatic amino acids and the so-called aromatic vitamins. Studies on ubiquinone synthesis and function led to an examination of oxidative phosphorylation and the structure and function of the F1F0-ATPase in the bacterium Escherichia coli. This work resulted in the formulation of a highly innovative model, involving rotating subunits of the F0 segment within the membrane and offering an explanation for the mechanism linking proton flow and ATP synthesis.

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Human surfactant protein B: structure, function, regulation, and genetic disease

Physiological Reviews ◽

10.1152/physrev.1995.75.4.749 ◽

1995 ◽

Vol 75 (4) ◽

pp. 749-757 ◽

Cited By ~ 138

Author(s):

J. A. Whitsett ◽

L. M. Nogee ◽

T. E. Weaver ◽

A. D. Horowitz

Keyword(s):

Gene Expression ◽

Surfactant Protein ◽

Structure And Function ◽

Respiratory Epithelial Cell ◽

Surfactant Protein B ◽

Cell Gene Expression ◽

Surfactant Phospholipids ◽

And Function ◽

Respiratory Epithelial ◽

Cell Gene

Elucidation of the structure and function of the hydrophobic surfactant protein (SP-B) and the SP-B gene has provided critical insight into surfactant homeostasis and control of respiratory epithelial cell gene expression. Surfactant protein B, in concert with surfactant protein A (SP-A), surfactant protein C (SP-C), and surfactant phospholipids, contributes to the structure and function of surfactant particles, determining surface activities and pathways by which surfactant phospholipids and proteins are processed, routed, packaged, and secreted from lamellar bodies by type II epithelial cells. After secretion, SP-B plays an essential role in determining the structure of tubular myelin, the stability and rapidity of spreading, and the recycling of surfactant phospholipids. The biochemical and structural signals underlying the homeostasis of alveolar surfactant are likely mediated by interactions between the surfactant proteins and phospholipids producing discrete structural forms that vary in size, aproprotein, and phospholipid content. Distinctions in structure, protein, and size are likely to determine the function of surfactant particles, their catabolism, or recycling by alveolar macrophages and airway epithelial cells. Analysis of the genetic controls governing the SP-B gene has led to the definition of DNA-protein interactions that determine respiratory epithelial cell gene expression in general. The important role of SP-B in lung function was defined by the study of a lethal neonatal respiratory disease, hereditary SP-B deficiency, caused by mutations in the human SP-B gene.

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