Combined bottom-up and top-down mass spectrometry analyses of the pattern of post-translational modifications of Drosophila melanogaster linker histone H1

Bonet-Costa, Carles; Vilaseca, Marta; Diema, Claudio; Vujatovic, Olivera; Vaquero, Alejandro; Omeñaca, Nuria; Castejón, Lucía; Bernués, Jordi; Giralt, Ernest; Azorı́n, Fernando

doi:10.1016/j.jprot.2012.05.034

Cited by 40 publications

(45 citation statements)

References 48 publications

(111 reference statements)

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“…Important functions for this domain are to be expected, first because it is present in all metazoan H1 subtypes and second because it harbors a large portion of the post-translational modifications described in metazoan (including Drosophila) H1 proteins (35,36). Our identification of a role for the NTD in promoting the formation of a single chromocenter in endoreplicating salivary gland cells begins to fill this gap.…”

Section: Discussionmentioning

confidence: 94%

Independent Biological and Biochemical Functions for Individual Structural Domains of Drosophila Linker Histone H1

Kavi¹,

Emelyanov

Fyodorov

et al. 2016

Journal of Biological Chemistry

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Linker histone H1 is among the most abundant components of chromatin. H1 has profound effects on chromosome architecture. H1 also helps to tether DNA-and histone-modifying enzymes to chromatin. Metazoan linker histones have a conserved tripartite structure comprising N-terminal, globular, and long, unstructured C-terminal domains. Here we utilize truncated Drosophila H1 polypeptides in vitro and H1 mutant transgenes in vivo to interrogate the roles of these domains in multiple biochemical and biological activities of H1. We demonstrate that the globular domain and the proximal part of the C-terminal domain are essential for H1 deposition into chromosomes and for the stability of H1-chromatin binding. The two domains are also essential for fly viability and the establishment of a normal polytene chromosome structure. Additionally, through interaction with the heterochromatin-specific histone H3 Lys-9 methyltransferase Su(var)3-9, the H1 C-terminal domain makes important contributions to formation and H3K9 methylation of heterochromatin as well as silencing of transposons in heterochromatin. Surprisingly, the N-terminal domain does not appear to be required for any of these functions. However, it is involved in the formation of a single chromocenter in polytene chromosomes. In summary, we have discovered that linker histone H1, similar to core histones, exerts its multiple biological functions through independent, biochemically separable activities of its individual structural domains.DNA in the eukaryotic nucleus is packaged into a compact nucleoprotein complex called chromatin (1, 2). The histones constitute a family of basic proteins that play a vital role in organizing chromatin. There are five major classes of histones: the core histones H2A, H2B, H3, and H4 and the linker histone H1. The nucleosome core particle, the fundamental unit of chromatin, consists of an octamer of two copies of each of the core histones around which about 146 bp of DNA is wrapped. H1 binds to the nucleosome core particle and the linker DNA between adjacent core particles. The stoichiometry of H1 to nucleosome core particles in cells of complex eukaryotes ranges from about 0.5 to approximately equimolar (3). Given this abundance, the linker histone H1 is expected to play important roles in chromatin structure. Indeed, numerous in vitro studies, as well as experiments in vivo, have shown that H1 has a profound effect on chromatin structure (reviewed in Refs. 4 and 5). For example, incorporation of H1 into chromatin leads to an increase in the spacing between nucleosome core particles. H1 also facilitates the folding of chromatin into more compact structures. In addition to these architectural roles, there are now an increasing number of reports describing interactions between H1 linker histones and a variety of other nuclear proteins (6), including functional interactions between H1, histone-modifying enzymes, and DNA methyltransferases that lead to modulation of epigenetic marking of chromatin (7,8). In this context, it is notable th...

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Section: Discussionmentioning

confidence: 94%

Independent Biological and Biochemical Functions for Individual Structural Domains of Drosophila Linker Histone H1

Kavi¹,

Emelyanov

Fyodorov

et al. 2016

Journal of Biological Chemistry

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“…Because CPRP-family peptides contain multiple arginine and lysine, trypsin digestion produces too short tryptic peptides to be detected by MS, and also it is challenging to assemble multiple tryptic peptides from a mixture. Bonet-Costa et al [45] reported an integrated top-down and bottom-up strategy to characterize histone proteins, where similar challenges exist in that the target proteins contain multiple basic amino acid residues. In our study, to sequence the mid-size CPRP peptides with multiple basic amino acid residues, we introduced a modified bottom-up de novo sequencing method.…”

Section: Resultsmentioning

confidence: 99%

A multi-scale strategy for discovery of novel endogenous neuropeptides in the crustacean nervous system

Jia

Lietz

et al. 2013

Journal of Proteomics

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The conventional mass spectrometry (MS)-based strategy is often inadequate for the comprehensive characterization of various size neuropeptides without assistance of genomic information. This study evaluated sequence coverage of different size neuropeptides in two crustacean species, blue crab Callinectes sapidus and Jonah crab Cancer borealis using conventional MS methodologies and revealed limitations to mid- and large-size peptide analysis. Herein we attempt to establish a multi-scale strategy for simultaneous and confident sequence elucidation of various sizes of peptides in the crustacean nervous system. Nine novel neuropeptides spanning a wide range of molecular weights (0.9-8.2 kDa) were fully sequenced from a major neuroendocrine organ, the sinus gland of the spiny lobster Panulirus interruptus. These novel neuropeptides included seven allatostatin (A- and B-type) peptides, one crustacean hyperglycemic hormone precursor-related peptide, and one crustacean hyperglycemic hormone. Highly accurate multi-scale characterization of a collection of varied size neuropeptides was achieved by integrating traditional data-dependent tandem MS, improved bottom-up sequencing, multiple fragmentation technique-enabled top-down sequencing, chemical derivatization, and in silico homology search. Collectively, the ability to characterize a neuropeptidome with vastly differing molecule sizes from a neural tissue extract could find great utility in unraveling complex signaling peptide mixtures employed by other biological systems.

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“…However nowadays, some top-down approaches are used in proteomics such as analyzing PTMs [65], mapping intact protein isoforms [124], etc. Some researchers also combined bottom-up and top-down mass spectrometry analysis of the histone PTMs, and their combinatorial patterns [18].…”

Section: Research Objective and Motivationmentioning

confidence: 99%

NBPMF: Novel network-based inference methods for peptide mass fingerprinting

Liang

Lajoie

Zhang

2017

2017 IEEE 16th International Conference on Cognitive Informatics &Amp; Cognitive Computing (ICCI*CC)

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Proteins are large, complex molecules that perform a vast array of functions in every living cell. A proteome is a set of proteins produced in an organism, and proteomics is the large-scale study of proteomes. Several high-throughput technologies have been developed in proteomics, where the most commonly applied are mass spectrometry (MS) based approaches.MS is an analytical technique for determining the composition of a sample. Recently it has become a primary tool for protein identification, quantification, and post translational modification (PTM) characterization in proteomics research. There are usually two different ways to identify proteins: top-down and bottom-up. Top-down approaches are based on subjecting intact protein ions and large fragment ions to tandem MS directly, while bottom-up methods are based on mass spectrometric analysis of peptides derived from proteolytic digestion, usually with trypsin.In bottom-up techniques, peptide mass fingerprinting (PMF) is widely used to identify proteins from MS dataset. Conventional PMF representatives such as probabilistic MOWSE algorithm, is based on mass distribution of tryptic peptides. In this thesis, we developed a novel network-based inference software termed NBPMF. By analyzing peptide-protein bipartite network, we designed new peptide protein matching score functions. We present two methods: the static one, ProbS, is based on an independent probability framework; and the dynamic one, HeatS, depicts input dataset as dependent peptides. Moreover, we use linear regression to adjust the matching score according to the masses of proteins. In addition, we consider the order of retention time to further correct the score function. In the post processing, we design two algorithms: assignment of peaks, and protein filtration. The former restricts that a peak can only be assigned to one peptide in order to reduce random matches; and the latter assumes each peak can only be assigned to one protein. In the result validation, we propose two new target-decoy search strategies to estimate the false discovery rate (FDR). The experiments on simulated, authentic, and simulated authentic dataset demonstrate that our NBPMF approaches lead to significantly improved performance compared to several state-of-the-art methods.i

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Combined bottom-up and top-down mass spectrometry analyses of the pattern of post-translational modifications of Drosophila melanogaster linker histone H1

Cited by 40 publications

References 48 publications

Independent Biological and Biochemical Functions for Individual Structural Domains of Drosophila Linker Histone H1

Independent Biological and Biochemical Functions for Individual Structural Domains of Drosophila Linker Histone H1

A multi-scale strategy for discovery of novel endogenous neuropeptides in the crustacean nervous system

NBPMF: Novel network-based inference methods for peptide mass fingerprinting

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