Abstract:
:In eukaryotes, methylation of nucleosomal histones and other nuclear proteins is a central aspect of chromatin structure and dynamics. The past 15 years have seen an enormous advance in our understanding of the biochemistry of these modifications, and of their role in establishing the epigenetic code. We provide a synthetic overview, from an evolutionary perspective, of the main players in the eukaryotic chromatin protein methylation system, with an emphasis on catalytic domains. Several components of the eukaryotic protein methylation system had their origins in bacteria. In particular, the Rossmann fold protein methylases (PRMTs and DOT1), and the LSD1 and jumonji-related demethylases and oxidases, appear to have emerged in the context of bacterial peptide methylation and hydroxylation systems. These systems were originally involved in synthesis of peptide secondary metabolites, such as antibiotics, toxins, and siderophores. The peptidylarginine deiminases appear to have been acquired by animals from bacterial enzymes that modify cell-surface proteins. SET domain methylases, which display the β-clip fold, apparently first emerged in prokaryotes from the SAF superfamily of carbohydrate-binding domains. However, even in bacteria, a subset of the SET domains might have evolved a chromatin-related role in conjunction with a BAF60a/b-like SWIB domain protein and topoisomerases. By the time of the last eukaryotic common ancestor, multiple SET and PRMT methylases were already in place and are likely to have mediated methylation at the H3K4, H3K9, H3K36, and H4K20 positions, and carried out both asymmetric and symmetric arginine dimethylation. Inference of H3K27 methylation in the ancestral eukaryote appears uncertain, though it was certainly in place a little later in eukaryotic evolution. Current data suggest that unlike SET methylases, which are universally present in eukaryotes, demethylases are not. They appear to be absent in the earliest-branching eukaryotic lineages, and emerged later along with several other chromatin proteins, such as the Dot1-methylase, prior to divergence of the kinetoplastid-heterolobosean lineage from the remaining eukaryotes. This period also corresponds to the point of origin of DNA cytosine methylation by DNMT1. Origin of major lineages of SET domains such as the Trithorax, Su(var)3-9, Ash1, SMYD, and TTLL12 and E(Z) might have played the initial role in the establishment of multiple distinct heterochromatic and euchromatic states that are likely to have been present, in some form, through much of eukaryotic evolution. Elaboration of these chromatin states might have gone hand-in-hand with acquisition of multiple jumonji-related and LSD1-like demethylases, and functional linkages with the DNA methylation and RNAi systems. Throughout eukaryotic evolution, there were several lineage-specific expansions of SET domain proteins, which might be related to a special transcription regulation process in trypanosomes, acquisition of new meiotic recombination hotspots in animals, and methylation and associated modifications of the diatom silaffin proteins involved in silica biomineralization. The use of specific domains to "read" the methylation marks appears to have been present in the ancestral eukaryote itself. Of these the chromo-like domains appear to have been acquired from bacterial secreted proteins that might have a role in binding cell-surface peptides or peptidoglycan. Domain architectures of the primary enzymes involved in the eukaryotic protein methylation system indicate key features relating to interactions with each other and other modifications in chromatin, such as acetylation. They also emphasize the profound functional distinction between the role of demethylation and deacetylation in regulation of chromatin dynamics.
journal_name
Prog Mol Biol Transl Scijournal_title
Progress in molecular biology and translational scienceauthors
Aravind L,Abhiman S,Iyer LMdoi
10.1016/B978-0-12-387685-0.00004-4subject
Has Abstractpub_date
2011-01-01 00:00:00pages
105-76eissn
1877-1173issn
1878-0814pii
B9780123876850000044journal_volume
101pub_type
杂志文章abstract::Mechanotransduction, the conversion of a mechanical stimulus into an electrical signal, is a central mechanism to several physiological functions in mammals. It relies on the function of mechanosensitive ion channels (MSCs). Although the first single-channel recording from MSCs dates back to 30 years ago, the identity...
journal_title:Progress in molecular biology and translational science
pub_type: 杂志文章,评审
doi:10.1016/bs.pmbts.2014.11.011
更新日期:2015-01-01 00:00:00
abstract::In this chapter, I shall discuss the genetics, mode of inheritance and molecular origin of several corneal dystrophies. ...
journal_title:Progress in molecular biology and translational science
pub_type: 杂志文章,评审
doi:10.1016/bs.pmbts.2015.04.004
更新日期:2015-01-01 00:00:00
abstract::Pathologic aggregates of tau protein are observed in several neurodegenerative diseases and are used to diagnose and stage disease postmortem. Recent advances in positron emission tomography radioligands allow for the detection of aggregated tau proteins in living persons. This chapter describes the development and ch...
journal_title:Progress in molecular biology and translational science
pub_type: 杂志文章,评审
doi:10.1016/bs.pmbts.2019.07.007
更新日期:2019-01-01 00:00:00
abstract::Amyloidosis is a generic term for a group of diseases characterized by deposits in different organ systems of insoluble materials composed mainly of distinct fibrillar proteins named amyloid. Besides amyloid, heparan sulfate proteoglycan (HSPG), is commonly found in most amyloid deposits, suggesting that HS/HSPG may b...
journal_title:Progress in molecular biology and translational science
pub_type: 杂志文章,评审
doi:10.1016/S1877-1173(10)93013-5
更新日期:2010-01-01 00:00:00
abstract::Alpha-fetoprotein (AFP) is a glycoprotein and belongs to the gene family of serum albumins. The serum AFP levels were found to be elevated in the sera of liver cancer patients in 1964 and were subsequently developed and used as a liver cancer biomarker. However, elevated serum AFP levels have been observed in patients...
journal_title:Progress in molecular biology and translational science
pub_type: 杂志文章
doi:10.1016/bs.pmbts.2019.01.001
更新日期:2019-01-01 00:00:00
abstract::Carbon nanotubes (CNTs) are cylinder-shaped allotropic forms of carbon, most widely produced under chemical vapor deposition. They possess astounding chemical, electronic, mechanical, and optical properties. Being among the most promising materials in nanotechnology, they are also likely to revolutionize medicine. Amo...
journal_title:Progress in molecular biology and translational science
pub_type: 杂志文章,评审
doi:10.1016/B978-0-12-416020-0.00005-X
更新日期:2011-01-01 00:00:00
abstract::Telomeres are long nucleotide repeats and protein complexes at the ends of chromosomes that are essential for maintaining chromosomal stability. They shorten with each cell division, and therefore, telomere length is a marker for cellular aging and senescence. Epidemiological research of telomeres investigates the rol...
journal_title:Progress in molecular biology and translational science
pub_type: 杂志文章,评审
doi:10.1016/B978-0-12-397898-1.00005-0
更新日期:2014-01-01 00:00:00
abstract::Ndsts (N-deacetylase/N-sulfotransferases) are enzymes responsible for N-sulfation during heparan sulfate (HS) and heparin biosynthesis. In this review, basic features of the Ndst1 enzyme are covered and a brief description of HS biosynthesis and its regulation is presented. Effects of Ndst1 deficiency on embryonic dev...
journal_title:Progress in molecular biology and translational science
pub_type: 杂志文章,评审
doi:10.1016/S1877-1173(10)93003-2
更新日期:2010-01-01 00:00:00
abstract::Single-molecule approaches permit an unrivalled view of how complex systems operate and have recently been used to understand DNA-protein interactions. These tools have enabled advances in a particularly challenging problem, the search for damaged sites on DNA. DNA repair proteins are present at the level of just a fe...
journal_title:Progress in molecular biology and translational science
pub_type: 杂志文章,评审
doi:10.1016/B978-0-12-387665-2.00001-8
更新日期:2012-01-01 00:00:00
abstract::Here we describe the principles of protein surgery and its application to the molecular design for regulating the protein conformation. We initially describe the Poincare duality that defines the basis of complementarity in the time-dependent geometrical space. Next we introduce the theory of protein surgery consistin...
journal_title:Progress in molecular biology and translational science
pub_type: 杂志文章
doi:10.1016/bs.pmbts.2020.08.004
更新日期:2020-01-01 00:00:00
abstract::Neurodegenerative diseases are complex, progressive disorders and affect millions of people worldwide, contributing significantly to the global burden of disease. In recent years, research has begun to investigate epigenetic mechanisms for a potential role in disease etiology. In this chapter, we describe the current ...
journal_title:Progress in molecular biology and translational science
pub_type: 杂志文章,评审
doi:10.1016/bs.pmbts.2018.04.008
更新日期:2018-01-01 00:00:00
abstract::The Wnt family of secreted glycoproteins participates in a wide array of biological processes, including cellular differentiation, proliferation, survival, apoptosis, adhesion, angiogenesis, hypertrophy, and aging. The canonical Wnt signaling primarily utilizes β-catenin-mediated activation of transcription, while the...
journal_title:Progress in molecular biology and translational science
pub_type: 杂志文章,评审
doi:10.1016/B978-0-12-398459-3.00007-1
更新日期:2012-01-01 00:00:00
abstract::A substantive volume of research on autism spectrum disorder (ASD) has emerged in recent years adding to our understanding of the etiopathological process. Preclinical models in mice and rats have been highly instrumental in modeling and dissecting the contributions of a multitude of known genetic and environmental ri...
journal_title:Progress in molecular biology and translational science
pub_type: 杂志文章
doi:10.1016/bs.pmbts.2020.04.016
更新日期:2020-01-01 00:00:00
abstract::Cell membrane-associated junctional complexes mediate cell-cell adhesion, intercellular interactions, and other fundamental processes required for proper embryo morphogenesis. Cadherins are calcium-dependent transmembrane proteins at the core of adherens junctions and are expressed in distinct spatiotemporal patterns ...
journal_title:Progress in molecular biology and translational science
pub_type: 杂志文章,评审
doi:10.1016/B978-0-12-394311-8.00013-3
更新日期:2013-01-01 00:00:00
abstract::Regulators of G protein signaling (RGS) comprise a diverse group of about 40 proteins which determine signaling amplitude and duration via modulation of receptor/G protein or receptor/effector coupling. Several members of the RGS family are expressed in the brain, where they have precise roles in regulation of importa...
journal_title:Progress in molecular biology and translational science
pub_type: 杂志文章,评审
doi:10.1016/S1877-1173(09)86010-9
更新日期:2009-01-01 00:00:00
abstract::Grifola frondosa, a polypore fungus that grows at the base of trees, is an edible and medicinal mushroom with a large fruiting body characterized by overlapping caps. Japanese scholars found that Grifola frondosa polysaccharide or D-fraction is the major biologically active ingredient, which is a protein-bound glucan ...
journal_title:Progress in molecular biology and translational science
pub_type: 杂志文章,评审
doi:10.1016/bs.pmbts.2019.02.010
更新日期:2019-01-01 00:00:00
abstract::Since the discovery of specialized T cells with regulatory function, harnessing the power of these cells to ameliorate autoimmunity has been a major goal. Here we collate the evidence that regulatory T cells (Treg) can inhibit Type 1 diabetes in animal models and humans. We discuss the anatomical sites and molecular m...
journal_title:Progress in molecular biology and translational science
pub_type: 杂志文章,评审
doi:10.1016/bs.pmbts.2015.08.004
更新日期:2015-01-01 00:00:00
abstract::Both genetic and environmental factors play roles in the development of refractive errors. Identification of genes involved in refractive errors may help in elucidating the underlying molecular mechanism related to both genetic defects and environmental pressure. Recent development of techniques for genome wide analys...
journal_title:Progress in molecular biology and translational science
pub_type: 杂志文章,评审
doi:10.1016/bs.pmbts.2015.05.007
更新日期:2015-01-01 00:00:00
abstract::The zinc-finger transcription factor KLF2 transduces the physical forces exerted by blood flow into molecular signals responsible for a wide range of biological responses. Following its initial recognition as a flow-responsive endothelial transcription factor, KLF2 is now known to be expressed in a range of cell types...
journal_title:Progress in molecular biology and translational science
pub_type: 杂志文章,评审
doi:10.1016/B978-0-12-386930-2.00007-0
更新日期:2014-01-01 00:00:00
abstract::In 1982, the Cech group discovered that an intron structure in an rRNA precursor of Tetrahymena thermophila is sufficient to complete splicing without assistance from proteins. This was the first moment that scientists recognized RNAs can have catalytic activities derived from their own unique three-dimensional struct...
journal_title:Progress in molecular biology and translational science
pub_type: 杂志文章,评审
doi:10.1016/bs.pmbts.2018.07.001
更新日期:2018-01-01 00:00:00
abstract::Neuroinflammation is thought to play a key role in the development and progression of neurodegenerative diseases such as Alzheimer's disease. Positron emission tomography (PET) is an in vivo imaging technique capable of studying the biochemical processes which provide the molecular basis of disease. PET imaging of neu...
journal_title:Progress in molecular biology and translational science
pub_type: 杂志文章,评审
doi:10.1016/bs.pmbts.2019.04.005
更新日期:2019-01-01 00:00:00
abstract::-1 Programmed ribosomal frameshifting is a translational recoding event in which ribosomes slip backward along messenger RNA presumably due to increased tension disrupting the codon-anticodon interaction at the ribosome's coding site. Single-molecule physical methods and recent experiments characterizing the physical ...
journal_title:Progress in molecular biology and translational science
pub_type: 杂志文章,评审
doi:10.1016/bs.pmbts.2015.11.003
更新日期:2016-01-01 00:00:00
abstract::The worldwide epidemic of metabolic disease indicates that a better understanding of the pathways contributing to the pathogenesis of this constellation of diseases need to be determined. Nuclear hormone receptors comprise a superfamily of ligand-activated transcription factors that control development, differentiatio...
journal_title:Progress in molecular biology and translational science
pub_type: 杂志文章,评审
doi:10.1016/S1877-1173(09)87001-4
更新日期:2009-01-01 00:00:00
abstract::The complexity of memory formation and its persistence is a phenomenon that has been studied intensely for centuries. Memory exists in many forms and is stored in various brain regions. Generally speaking, memories are reorganized into broadly distributed cortical networks over time through systems level consolidation...
journal_title:Progress in molecular biology and translational science
pub_type: 杂志文章,评审
doi:10.1016/B978-0-12-420170-5.00005-2
更新日期:2014-01-01 00:00:00
abstract::Cerebral amyloid angiopathy (CAA) is commonly found in older people and in patients with Alzheimer's disease (AD) accompanying cerebrovascular disorders and dementia. Early-onset CAA cases generally have been found only in rare genetic forms of CAA. Interestingly, however, CAA-related hemorrhages have been recently re...
journal_title:Progress in molecular biology and translational science
pub_type: 杂志文章,评审
doi:10.1016/bs.pmbts.2019.05.012
更新日期:2019-01-01 00:00:00
abstract::Experimental data accumulated during the last 10 years strongly support the existence and functional significance of oligomerization of G protein-coupled receptors (GPCRs). In this essay, we discuss the unique biochemical properties of GPCR oligomers in the frame of "allosterism" and how these properties can be used t...
journal_title:Progress in molecular biology and translational science
pub_type: 杂志文章,评审
doi:10.1016/bs.pmbts.2019.11.006
更新日期:2020-01-01 00:00:00
abstract::Insulin resistance plays a key role in the development of type 2 diabetes mellitus and is also associated with several other diseases, such as obesity, hypertension, and cardiovascular diseases. Type 2 diabetes and obesity have become epidemic worldwide in the past few decades, and epidemiological and metabolic eviden...
journal_title:Progress in molecular biology and translational science
pub_type: 杂志文章,评审
doi:10.1016/B978-0-12-800101-1.00008-9
更新日期:2014-01-01 00:00:00
abstract::MicroRNAs (miRNAs) are small non-coding RNA molecules that have emerged in recent years as central regulators of eukaryotic gene expression. In mammalian systems, miRNAs are associated with numerous pathological and physiological pathways. miRNAs are important in many viral infections, with different viral families ex...
journal_title:Progress in molecular biology and translational science
pub_type: 杂志文章,评审
doi:10.1016/B978-0-12-415795-8.00002-7
更新日期:2011-01-01 00:00:00
abstract::The production of transgenic mice expressing different forms of the prion protein (PrP) or devoid of PrP has enabled researchers to study the role of PrP in the infectious process of a prion disease and its normal function in the healthy individual. A wide range of transgenic models have been produced ranging from PrP...
journal_title:Progress in molecular biology and translational science
pub_type: 杂志文章,评审
doi:10.1016/bs.pmbts.2017.06.008
更新日期:2017-01-01 00:00:00
abstract::Bombesin (Bn) is a 14-amino acid peptide isolated from the skin of the frog Bombina bombina. The mammalian homologs of this peptide include three forms of gastrin-releasing peptide (GRP): GRP-10, GRP-27, and GRP-29, and a 10-amino acid peptide referred to as neuromedin-B (NMB). These peptides evoke a number of respons...
journal_title:Progress in molecular biology and translational science
pub_type: 杂志文章,评审
doi:10.1016/B978-0-12-386933-3.00010-8
更新日期:2013-01-01 00:00:00