Specific Eukaryotic Genes: Structural Organisation and Function

Background Eukaryotic genes typically form independent evolutionary lineages through either speciation or gene duplication events. Generally, gene copies resulting from speciation events (orthologs) are expected to maintain similarity over time with regard to sequence, structure and function. After a duplication event, however, resulting gene copies (paralogs) may experience a broader set of possible fates, including partial (subfunctionalization) or complete loss of function, as well as gain of new function (neofunctionalization). This assumption, known as the Ortholog Conjecture, is prevalent throughout molecular biology and notably plays an important role in many functional annotation methods. Unfortunately, studies that explicitly compare evolutionary processes between speciation and duplication events are rare and conflicting. Methods To provide an empirical assessment of ortholog/paralog evolution, we estimated ratios of nonsynonymous to synonymous substitutions (ω = dN/dS) for 251,044 lineages in 6,244 gene trees across 77 vertebrate taxa. Results Overall, we found ω to be more similar between lineages descended from speciation events (p < 0.001) than lineages descended from duplication events, providing strong support for the Ortholog Conjecture. The asymmetry in ω following duplication events appears to be largely driven by an increase along one of the paralogous lineages, while the other remains similar to the parent. This trend is commonly associated with neofunctionalization, suggesting that gene duplication is a significant mechanism for generating novel gene functions.

Download Full-text

Micro RNAS as New Players in Control of Hypothalamic Functions

Creative Surgery and Oncology ◽

10.24060/2076-3093-2019-9-2-138-143 ◽

2019 ◽

Vol 9 (2) ◽

pp. 138-143

Author(s):

O. A. Beylerli ◽

I. F. Gareev ◽

A. T. Beylerli

Keyword(s):

Regulation Of Gene Expression ◽

Vital Role ◽

Key Factors ◽

Eukaryotic Genes ◽

Micro Rnas ◽

A Cell ◽

The Central Nervous System ◽

And Function ◽

Post Transcriptional Regulation

Micro RNAs (miRNAs) are short non-coding RNAs (ncRNAs) of ~22 nucleotides in length involved in the post-transcriptional regulation of gene expression. They were discovered over 15 years ago and their functions are becoming clearer. They play an important role in all biological processes. MiRNAs are important modulators of the expression of eukaryotic genes. Focusing on transcripts encoding proteins they impact on the cellular transcriptome thus helping to determine the destiny of a cell. More and more data emerge to indicate an important functional role of miRNAs in the brain development. Since their discovery many miRNAs have been described as key factors in the development and function of the central nervous system. Some play a significant role in the genesis and differentiation of nerve cells (neurons and glial cells). Notably, it has recently been established that miRNAs play a vital role in the mechanisms underpinning the infantile increase of the gonadotropin-releasing hormone (GnRH) production by neurons in the hypothalamus. This phenomenon is necessary for the onset of puberty in mammals. In this review offers our attempt to describe miRNAs as new players in the control of hypothalamic functions, namely the onset of puberty.

Download Full-text

Stress Induction and Mitochondrial Localization of Oxr1 Proteins in Yeast and Humans

Molecular and Cellular Biology ◽

10.1128/mcb.24.8.3180-3187.2004 ◽

2004 ◽

Vol 24 (8) ◽

pp. 3180-3187 ◽

Cited By ~ 57

Author(s):

Nathan A. Elliott ◽

Michael R. Volkert

Keyword(s):

Oxidative Damage ◽

Aerobic Respiration ◽

Oxygen Species ◽

Mitochondrial Localization ◽

Stress Induction ◽

Cellular Processes ◽

Eukaryotic Genes ◽

As Stress ◽

And Function ◽

And Oxidative Stress

ABSTRACT Reactive oxygen species (ROS) are critical molecules produced as a consequence of aerobic respiration. It is essential for cells to control the production and activity of such molecules in order to protect the genome and regulate cellular processes such as stress response and apoptosis. Mitochondria are the major source of ROS within the cell, and as a result, numerous proteins have evolved to prevent or repair oxidative damage in this organelle. The recently discovered OXR1 gene family represents a set of conserved eukaryotic genes. Previous studies of the yeast OXR1 gene indicate that it functions to protect cells from oxidative damage. In this report, we show that human and yeast OXR1 genes are induced by heat and oxidative stress and that their proteins localize to the mitochondria and function to protect against oxidative damage. We also demonstrate that mitochondrial localization is required for Oxr1 protein to prevent oxidative damage.

Download Full-text

Structure and function of eukaryotic genes

Nature ◽

10.1038/282015a0 ◽

1979 ◽

Vol 282 (5734) ◽

pp. 15-15 ◽

Cited By ~ 1

Author(s):

Jonathan Wolfe

Keyword(s):

Structure And Function ◽

Eukaryotic Genes ◽

And Function

Download Full-text

Recent advances in understanding RNA polymerase II structure and function

Faculty Reviews ◽

10.12703/b/9-11 ◽

2020 ◽

Vol 9 ◽

Author(s):

Daniel Reines

Keyword(s):

Rna Polymerase ◽

Rna Polymerase Ii ◽

New Technologies ◽

Firing Frequency ◽

Initiation Factors ◽

Intrinsically Disordered ◽

Eukaryotic Genes ◽

Transcription Process ◽

And Function ◽

Aggregate Population

More than 50 years after the identification of RNA polymerase II, the enzyme responsible for the transcription of most eukaryotic genes, studies have continued to reveal fresh aspects of its structure and regulation. New technologies, coupled with years of development of a vast catalog of RNA polymerase II accessory proteins and activities, have led to new revelations about the transcription process. The maturation of cryo-electron microscopy as a tool for unraveling the detailed structure of large molecular machines has provided numerous structures of the enzyme and its accessory factors. Advances in biophysical methods have enabled the observation of a single polymerase’s behavior, distinct from work on aggregate population averages. Other recent work has revealed new properties and activities of the general initiation factors that RNA polymerase II employs to accurately initiate transcription, as well as chromatin proteins that control RNA polymerase II’s firing frequency, and elongation factors that facilitate the enzyme’s departure from the promoter and which control sequential steps and obstacles that must be navigated by elongating RNA polymerase II. There has also been a growing appreciation of the physical properties conferred upon many of these proteins by regions of each polypeptide that are of low primary sequence complexity and that are often intrinsically disordered. This peculiar feature of a surprisingly large number of proteins enables a disordered region of the protein to morph into a stable structure and creates an opportunity for pathway participants to dynamically partition into subcompartments of the nucleus. These subcompartments host designated portions of the chemical reactions that lead to mRNA synthesis. This article highlights a selection of recent findings that reveal some of the resolved workings of RNA polymerase II and its ensemble of supporting factors.

Download Full-text

Conformation of Ribosomes from Escherichia Coli

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100051062 ◽

1974 ◽

Vol 32 ◽

pp. 210-211

Author(s):

M. Boublik ◽

W. Hellmann ◽

F. Jenkins

Keyword(s):

Binding Sites ◽

Ribosomal Proteins ◽

Fluorescent Dyes ◽

Protein Biosynthesis ◽

Three Dimensional ◽

Spatial Arrangement ◽

Dimensional Structure ◽

Complete Understanding ◽

And Function

The present knowledge of the three-dimensional structure of ribosomes is far too limited to enable a complete understanding of the various roles which ribosomes play in protein biosynthesis. The spatial arrangement of proteins and ribonuclec acids in ribosomes can be analysed in many ways. Determination of binding sites for individual proteins on ribonuclec acid and locations of the mutual positions of proteins on the ribosome using labeling with fluorescent dyes, cross-linking reagents, neutron-diffraction or antibodies against ribosomal proteins seem to be most successful approaches. Structure and function of ribosomes can be correlated be depleting the complete ribosomes of some proteins to the functionally inactive core and by subsequent partial reconstitution in order to regain active ribosomal particles.

Download Full-text

The Effect of Oxidized Cholesterol on the Aorta of Rabbits- Scanning Electron Microscopic Observations

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100054327 ◽

1982 ◽

Vol 40 ◽

pp. 340-341

Author(s):

S. K. Pena ◽

C. B. Taylor ◽

J. Hill ◽

J. Safarik

Keyword(s):

Cholesterol Biosynthesis ◽

Cholesterol Content ◽

Arterial Injury ◽

Electron Microscopic ◽

Aortic Smooth Muscle ◽

Oxidized Cholesterol ◽

Initial Event ◽

Membrane Structure And Function ◽

Scanning Electron Microscopic ◽

And Function

Introduction: Oxidized cholesterol derivatives have been demonstrated in various cell cultures to be very potent inhibitors of 3-hvdroxy-3- methylglutaryl Coenzyme A reductase which is a principle regulator of cholesterol biosynthesis in the cell. The cholesterol content in the cells exposed to oxidized cholesterol was found to be markedly decreased. In aortic smooth muscle cells, the potency of this effect was closely related to the cytotoxicity of each derivative. Furthermore, due to the similarity of their molecular structure to that of cholesterol, these oxidized cholesterol derivatives might insert themselves into the cell membrane, alter membrane structure and function and eventually cause cell death. Arterial injury has been shown to be the initial event of atherosclerosis.

Download Full-text

Ultrastructure of developing visual cortical synapses in the cat superior colliculus

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100085083 ◽

1991 ◽

Vol 49 ◽

pp. 156-157

Author(s):

Caroline A. Miller ◽

Laura L. Bruce

Keyword(s):

Superior Colliculus ◽

Phosphate Buffer ◽

Receptive Fields ◽

Visual Cortical Area ◽

Cortical Synapses ◽

Visual Cortical ◽

And Function ◽

Phosphate Buffered Saline ◽

The Brain ◽

Cat Superior Colliculus

The first visual cortical axons arrive in the cat superior colliculus by the time of birth. Adultlike receptive fields develop slowly over several weeks following birth. The developing cortical axons go through a sequence of changes before acquiring their adultlike morphology and function. To determine how these axons interact with neurons in the colliculus, cortico-collicular axons were labeled with biocytin (an anterograde neuronal tracer) and studied with electron microscopy.Deeply anesthetized animals received 200-500 nl injections of biocytin (Sigma; 5% in phosphate buffer) in the lateral suprasylvian visual cortical area. After a 24 hr survival time, the animals were deeply anesthetized and perfused with 0.9% phosphate buffered saline followed by fixation with a solution of 1.25% glutaraldehyde and 1.0% paraformaldehyde in 0.1M phosphate buffer. The brain was sectioned transversely on a vibratome at 50 μm. The tissue was processed immediately to visualize the biocytin.

Download Full-text