scholarly journals Post-translational Modifications in Oral Bacteria and Their Functional Impact

2021 ◽  
Vol 12 ◽  
Author(s):  
Qizhao Ma ◽  
Qiong Zhang ◽  
Yang Chen ◽  
Shuxing Yu ◽  
Jun Huang ◽  
...  
Keyword(s):  
Virulence Factors ◽  
Regulatory Networks ◽  
Oral Bacteria ◽  
Amino Acid Residues ◽  
Post Translational Modifications ◽  
Physiological Processes ◽  
The Face ◽  
Domains Of Life ◽  
And Function ◽  
External Stimuli

Oral bacteria colonize the oral cavity, surrounding complex and variable environments. Post-translational modifications (PTMs) are an efficient biochemical mechanism across all domains of life. Oral bacteria could depend on PTMs to quickly regulate their metabolic processes in the face of external stimuli. In recent years, thanks to advances in enrichment strategies, the number and variety of PTMs that have been identified and characterized in oral bacteria have increased. PTMs, covalently modified by diverse enzymes, occur in amino acid residues of the target substrate, altering the functions of proteins involved in different biological processes. For example, Ptk1 reciprocally phosphorylates Php1 on tyrosine residues 159 and 161, required for Porphyromonas gingivalis EPS production and community development with the antecedent oral biofilm constituent Streptococcus gordonii, and in turn Php1 dephosphorylates Ptk1 and rapidly causes the conversion of Ptk1 to a state of low tyrosine phosphorylation. Protein acetylation is also widespread in oral bacteria. In the acetylome of Streptococcus mutans, 973 acetylation sites were identified in 445 proteins, accounting for 22.7% of overall proteins involving virulence factors and pathogenic processes. Other PTMs in oral bacteria include serine or threonine glycosylation in Cnm involving intracerebral hemorrhage, arginine citrullination in peptidylarginine deiminases (PADs), leading to inflammation, lysine succinylation in P. gingivalis virulence factors (gingipains, fimbriae, RagB, and PorR), and cysteine glutathionylation in thioredoxin-like protein (Tlp) in response to oxidative stress in S. mutans. Here we review oral bacterial PTMs, focusing on acetylation, phosphorylation, glycosylation, citrullination, succinylation, and glutathionylation, and corresponding modifying enzymes. We describe different PTMs in association with some examples, discussing their potential role and function in oral bacteria physiological processes and regulatory networks. Identification and characterization of PTMs not only contribute to understanding their role in oral bacterial virulence, adaption, and resistance but will open new avenues to treat oral infectious diseases.

scholarly journals The Importance of GLWamide Neuropeptides in Cnidarian Development and Physiology

2011 ◽  
Vol 2011 ◽  
pp. 1-8 ◽  
Author(s):  
Toshio Takahashi ◽  
Masayuki Hatta
Keyword(s):  
Basic Structure ◽  
Signaling Molecules ◽  
Structure And Function ◽  
Amino Acid Residues ◽  
Peptide Signaling ◽  
Physiological Processes ◽  
History Of ◽  
Species Specific ◽  
And Function ◽  
Potential Use

The peptide-signaling molecules (<50 amino acid residues) occur in a wide variety of invertebrate and vertebrate organisms, playing pivotal roles in physiological, endocrine, and developmental processes. While some of these peptides display similar structures in mammals and invertebrates, others differ with respect to their structure and function in a species-specific manner. Such a conservation of basic structure and function implies that many peptide-signaling molecules arose very early in the evolutionary history of some taxa, while species-specific characteristics led us to suggest that they also acquire the ability to evolve in response to specific environmental conditions. In this paper, we describe GLWamide-family peptides that function as signaling molecules in the process of muscle contraction, metamorphosis, and settlement in cnidarians. The peptides are produced by neurons and are therefore referred to as neuropeptides. We discuss the importance of the neuropeptides in both developmental and physiological processes in a subset of hydrozoans, as well as the potential use as a seed compound in drug development and aspects related to the protection of corals.

scholarly journals Protein and Proteome Atlas for Plants under Stresses: New Highlights and Ways for Integrated Omics in Post-Genomics Era

2019 ◽  
Vol 20 (20) ◽  
pp. 5222 ◽  
Author(s):  
Xuchu Wang
Keyword(s):  
Protein Identification ◽  
Target Genes ◽  
Protein Quantification ◽  
Plant Proteins ◽  
Post Translational Modifications ◽  
Physiological Processes ◽  
Integrated Omics ◽  
Response To Stress ◽  
And Function ◽  
Integrative Omics

In the post-genomics era, integrative omics studies for biochemical, physiological, and molecular changes of plants in response to stress conditions play more crucial roles. Among them, atlas analysis of plants under different abiotic stresses, including salinity, drought, and toxic conditions, has become more important for uncovering the potential key genes and proteins in different plant tissues. High-quality genomic data and integrated analyses of transcriptomic, proteomic, metabolomics, and phenomic patterns provide a deeper understanding of how plants grow and survive under environmental stresses. This editorial mini-review aims to synthesize the 27 papers including two timely reviews that have contributed to this Special Issue, which focuses on concluding the recent progress in the Protein and Proteome Atlas in plants under different stresses. It covers various aspects of plant proteins ranging from agricultural proteomics, structure and function of proteins, novel techniques and approaches for gene and protein identification, protein quantification, proteomics for post-translational modifications (PTMs), and new insights into proteomics. The proteomics-based results in this issue will help the readers to gain novel insights for the understanding of complicated physiological processes in crops and other important plants in response to stressed conditions. Furthermore, these target genes and proteins that are important candidates for further functional validation in economic plants and crops can be studied.

scholarly journals Mutually exclusive locales for N-linked glycans and disorder in glycoproteins

2018 ◽  
Author(s):  
Alvina Singh ◽  
Indu Kumari ◽  
Dharma Pally ◽  
Shyamili Goutham ◽  
Sujasha Ghosh ◽  
...  
Keyword(s):  
Amino Acid ◽  
Protein Stability ◽  
Amino Acid Residue ◽  
Tertiary Structure ◽  
Amino Acid Residues ◽  
Mutual Exclusivity ◽  
Post Translational Modifications ◽  
Phylogenetic Conservation ◽  
And Function ◽  
Disordered Regions

AbstractSeveral post-translational modifications of proteins lie within regions of disorder, stretches of amino acid residues that exhibit a dynamic tertiary structure and resist crystallization. Such localization has been proposed to expand the binding versatility of the disordered regions, and hence, the repertoire of interacting partners for the proteins. However, investigating a dataset of 500 human N-linked glycoproteins, we observed that the sites of N-linked glycosylations, or N-glycosites, lay predominantly within the regions of predicted order rather than their unstructured counterparts. This mutual exclusivity between disordered stretches and N-glycosites could not be reconciled merely through asymmetry in distribution of asparagines, serines or threonines residues, which comprise the minimum-required signature for conjugation by N-linked glycans, but rather by a contextual enrichment of these residues next to each other within the ordered portions. In fact, N-glycosite neighborhoods and disordered stretches showed distinct sets of enriched residues suggesting their individualized roles in protein phenotype. N-glycosite neighborhood residues also showed higher phylogenetic conservation than disordered stretches within amniote orthologs of glycoproteins. However, a universal search for residue-combinations that are putatively domain-constitutive ranked the disordered regions higher than the N-glycosite neighborhoods. We propose that amino acid residue-combinations bias the permissivity for N-glycoconjugation within ordered regions, so as to balance the tradeoff between the evolution of protein stability, and function, contributed by the N-linked glycans and disordered regions respectively.

scholarly journals Phosphorylation and Circadian Molecular Timing

2020 ◽  
Vol 11 ◽  
Author(s):  
Andrea Brenna ◽  
Urs Albrecht
Keyword(s):  
Circadian Rhythms ◽  
Circadian Clock ◽  
Environmental Changes ◽  
Circadian System ◽  
Post Translational Modifications ◽  
Physiological Processes ◽  
Clock Proteins ◽  
Protein Components ◽  
Response To Environmental Change ◽  
External Stimuli

Endogenous circadian rhythms are biological processes generated by an internal body clock. They are self-sustaining, and they govern biochemical and physiological processes. However, circadian rhythms are influenced by many external stimuli to reprogram the phase in response to environmental change. Through their adaptability to environmental changes, they synchronize physiological responses to environmental challenges that occur within a sidereal day. The precision of this circadian system is assured by many post-translational modifications (PTMs) that occur on the protein components of the circadian clock mechanism. The most ancient example of circadian rhythmicity driven by phosphorylation of clock proteins was observed in cyanobacteria. The influence of phosphorylation on the circadian system is observed through different kingdoms, from plants to humans. Here, we discuss how phosphorylation modulates the mammalian circadian clock, and we give a detailed overview of the most critical discoveries in the field.

A ribosomally synthesized and post-translationally modified peptide containing a β-amino acid and a macrocyclic motif

2021 ◽  
Author(s):  
Shan Wang ◽  
Qing Fang ◽  
Roland Gyampoh ◽  
Zhou Lu ◽  
Yingli Gao ◽  
...  
Keyword(s):  
Amino Acid ◽  
Computational Modelling ◽  
Genomic Analysis ◽  
Structural Diversity ◽  
Biosynthetic Gene Cluster ◽  
Amino Acid Residues ◽  
Post Translational Modifications ◽  
Gram Positive Bacteria ◽  
Modified Peptides ◽  
Domains Of Life

Abstract Ribosomally synthesized and post-translationally modified peptides (RiPPs) are structurally complex naturally occurring metabolites across all three domains of life. Despite the structural diversity of RiPPs that stems from the extensive post-translational modifications, only α-amino acid residues have been found in known RiPPs. Here we report discovery of a new 27-mer peptide, kintamdin, using comprehensive MS and NMR structural elucidation and genomic analysis together with computational modelling. The peptide features a β-amino acid residue and a new thioether macrocyclic ring. Heterologous expression and gene inactivation allowed the identification of the minimal biosynthetic gene cluster (BGC). The gene products in kin BGC share low homologues compared to other known RiPP pathways, further rendering the novelty of kintamdin. Biochemical analysis indicated that KinO mediate di-methylation reaction to yield kintamidn. Finally, the occurrence of the kin-like BGCs in Gram-positive bacteria suggested the biological importance of this new group of RiPPs.

scholarly journals Halomethyl-Triazoles for Rapid, Site-Selective Protein Modification

Molecules ◽  
2021 ◽  
Vol 26 (18) ◽  
pp. 5461
Author(s):  
Richard C. Brewster ◽  
Alison N. Hulme
Keyword(s):  
Protein Modification ◽  
Protein Translation ◽  
Cysteine Residue ◽  
Amino Acid Residues ◽  
Post Translational Modifications ◽  
Select Amino Acid ◽  
Methionine Residues ◽  
And Function ◽  
Alkylating Reagents ◽  
Site Selective

Post-translational modifications (PTMs) are used by organisms to control protein structure and function after protein translation, but their study is complicated and their roles are not often well understood as PTMs are difficult to introduce onto proteins selectively. Designing reagents that are both good mimics of PTMs, but also only modify select amino acid residues in proteins is challenging. Frequently, both a chemical warhead and linker are used, creating a product that is a misrepresentation of the natural modification. We have previously shown that biotin-chloromethyl-triazole is an effective reagent for cysteine modification to give S-Lys derivatives where the triazole is a good mimic of natural lysine acylation. Here, we demonstrate both how the reactivity of the alkylating reagents can be increased and how the range of triazole PTM mimics can be expanded. These new iodomethyl-triazole reagents are able to modify a cysteine residue on a histone protein with excellent selectivity in 30 min to give PTM mimics of acylated lysine side-chains. Studies on the more complicated, folded protein SCP-2L showed promising reactivity, but also suggested the halomethyl-triazoles are potent alkylators of methionine residues.

scholarly journals Connection Between Chromosomal Location and Function of CtrA Phosphorelay Genes in Alphaproteobacteria

2021 ◽  
Vol 12 ◽  
Author(s):  
Jürgen Tomasch ◽  
Sonja Koppenhöfer ◽  
Andrew S. Lang
Keyword(s):  
Regulatory Networks ◽  
Caulobacter Crescentus ◽  
Response Regulator ◽  
Regulatory System ◽  
Physiological Processes ◽  
Gene Regulatory System ◽  
Bacterial Chromosomes ◽  
Differential Positioning ◽  
Gene Regulatory ◽  
And Function

Most bacterial chromosomes are circular, with replication starting at one origin (ori) and proceeding on both replichores toward the terminus (ter). Several studies have shown that the location of genes relative to ori and ter can have profound effects on regulatory networks and physiological processes. The CtrA phosphorelay is a gene regulatory system conserved in most alphaproteobacteria. It was first discovered in Caulobacter crescentus where it controls replication and division into a stalked and a motile cell in coordination with other factors. The locations of the ctrA gene and targets of this response regulator on the chromosome affect their expression through replication-induced DNA hemi-methylation and specific positioning along a CtrA activity gradient in the dividing cell, respectively. Here we asked to what extent the location of CtrA regulatory network genes might be conserved in the alphaproteobacteria. We determined the locations of the CtrA phosphorelay and associated genes in closed genomes with unambiguously identifiable ori from members of five alphaproteobacterial orders. The location of the phosphorelay genes was the least conserved in the Rhodospirillales followed by the Sphingomonadales. In the Rhizobiales a trend toward certain chromosomal positions could be observed. Compared to the other orders, the CtrA phosphorelay genes were conserved closer to ori in the Caulobacterales. In contrast, the genes were highly conserved closer to ter in the Rhodobacterales. Our data suggest selection pressure results in differential positioning of CtrA phosphorelay and associated genes in alphaproteobacteria, particularly in the orders Rhodobacterales, Caulobacterales and Rhizobiales that is worth deeper investigation.

Dicarbonyl derived post-translational modifications: chemistry bridging biology and aging-related disease

2020 ◽  
Vol 64 (1) ◽  
pp. 97-110
Author(s):  
Christian Sibbersen ◽  
Mogens Johannsen
Keyword(s):  
Mass Spectrometry ◽  
Future Research ◽  
Amino Acid Residues ◽  
Post Translational Modification ◽  
Dicarbonyl Compounds ◽  
Protein Targets ◽  
Post Translational Modifications ◽  
Reactive Protein ◽  
Glycation End Products ◽  
Direct Mass Spectrometry

Abstract In living systems, nucleophilic amino acid residues are prone to non-enzymatic post-translational modification by electrophiles. α-Dicarbonyl compounds are a special type of electrophiles that can react irreversibly with lysine, arginine, and cysteine residues via complex mechanisms to form post-translational modifications known as advanced glycation end-products (AGEs). Glyoxal, methylglyoxal, and 3-deoxyglucosone are the major endogenous dicarbonyls, with methylglyoxal being the most well-studied. There are several routes that lead to the formation of dicarbonyl compounds, most originating from glucose and glucose metabolism, such as the non-enzymatic decomposition of glycolytic intermediates and fructosyl amines. Although dicarbonyls are removed continuously mainly via the glyoxalase system, several conditions lead to an increase in dicarbonyl concentration and thereby AGE formation. AGEs have been implicated in diabetes and aging-related diseases, and for this reason the elucidation of their structure as well as protein targets is of great interest. Though the dicarbonyls and reactive protein side chains are of relatively simple nature, the structures of the adducts as well as their mechanism of formation are not that trivial. Furthermore, detection of sites of modification can be demanding and current best practices rely on either direct mass spectrometry or various methods of enrichment based on antibodies or click chemistry followed by mass spectrometry. Future research into the structure of these adducts and protein targets of dicarbonyl compounds may improve the understanding of how the mechanisms of diabetes and aging-related physiological damage occur.

Matrix Metalloproteinases in Invertebrates

2020 ◽  
Vol 27 (11) ◽  
pp. 1068-1081
Author(s):  
Xi Liu ◽  
Dongwu Liu ◽  
Yangyang Shen ◽  
Mujie Huang ◽  
Lili Gao ◽  
...  
Keyword(s):  
Matrix Metalloproteinases ◽  
Immune Responses ◽  
Theoretical Basis ◽  
Regulatory Mechanism ◽  
Structure And Function ◽  
Catalytic Domains ◽  
Physiological Processes ◽  
Disease Occurrence ◽  
Complex Functions ◽  
And Function

Matrix Metalloproteinases (MMPs) belong to a family of metal-dependent endopeptidases which contain a series of conserved pro-peptide domains and catalytic domains. MMPs have been widely found in plants, animals, and microorganisms. MMPs are involved in regulating numerous physiological processes, pathological processes, and immune responses. In addition, MMPs play a key role in disease occurrence, including tumors, cardiovascular diseases, and other diseases. Compared with invertebrate MMPs, vertebrate MMPs have diverse subtypes and complex functions. Therefore, it is difficult to study the function of MMPs in vertebrates. However, it is relatively easy to study invertebrate MMPs because there are fewer subtypes of MMPs in invertebrates. In the present review, the structure and function of MMPs in invertebrates were summarized, which will provide a theoretical basis for investigating the regulatory mechanism of MMPs in invertebrates.

scholarly journals Disentangling transcriptional responses in plant defense against arthropod herbivores

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Alejandro Garcia ◽  
M. Estrella Santamaria ◽  
Isabel Diaz ◽  
Manuel Martinez
Keyword(s):  
Regulatory Networks ◽  
Pieris Rapae ◽  
Meta Analysis ◽  
Plant Response ◽  
Plant Responses ◽  
Transcriptional Responses ◽  
Crop Species ◽  
Physiological Processes ◽  
Meta Analyses ◽  
Plant Herbivore

AbstractThe success in the response of a plant to a pest depends on the regulatory networks that connect plant perception and plant response. Meta-analyses of transcriptomic responses are valuable tools to discover novel mechanisms in the plant/herbivore interplay. Considering the quantity and quality of available transcriptomic analyses, Arabidopsis thaliana was selected to test the ability of comprehensive meta-analyses to disentangle plant responses. The analysis of the transcriptomic data showed a general induction of biological processes commonly associated with the response to herbivory, like jasmonate signaling or glucosinolate biosynthesis. However, an uneven induction of many genes belonging to these biological categories was found, which was likely associated with the particularities of each specific Arabidopsis-herbivore interaction. A thorough analysis of the responses to the lepidopteran Pieris rapae and the spider mite Tetranychus urticae highlighted specificities in the perception and signaling pathways associated with the expression of receptors and transcription factors. This information was translated to a variable alteration of secondary metabolic pathways. In conclusion, transcriptomic meta-analysis has been revealed as a potent way to sort out relevant physiological processes in the plant response to herbivores. Translation of these transcriptomic-based analyses to crop species will permit a more appropriate design of biotechnological programs.

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