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Frando A, Grundner C. More than two components: complexities in bacterial phosphosignaling. mSystems 2024; 9:e0028924. [PMID: 38591891 PMCID: PMC11097640 DOI: 10.1128/msystems.00289-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/10/2024] Open
Abstract
For over 40 years, the two-component systems (TCSs) have taken front and center in our thinking about the signaling mechanisms by which bacteria sense and respond to their environment. In contrast, phosphorylation on Ser/Thr and Tyr (O-phosphorylation) was long thought to be mostly restricted to eukaryotes and a somewhat accessory signaling mechanism in bacteria. Several recent studies exploring systems aspects of bacterial O-phosphorylation, however, now show that it is in fact pervasive, with some bacterial proteomes as highly phosphorylated as those of eukaryotes. Labile, non-canonical protein phosphorylation sites on Asp, Arg, and His are now also being identified in large numbers in bacteria and first cellular functions are discovered. Other phosphomodifications on Cys, Glu, and Lys remain largely unexplored. The surprising breadth and complexity of bacterial phosphosignaling reveals a vast signaling capacity, the full scope of which we may only now be beginning to understand but whose functions are likely to affect all aspects of bacterial physiology and pathogenesis.
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Affiliation(s)
- Andrew Frando
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, USA
| | - Christoph Grundner
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, USA
- Department of Pediatrics, University of Washington, Seattle, Washington, USA
- Department of Global Health, University of Washington, Seattle, Washington, USA
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2
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Diptiman D, Jalan A, Pal R, Dodwani S, Bandyopadhyay D. Hist-i-fy-a multiple histidine post-translational-modification (PTM) prediction server based on protein sequences using convolution neural network: a case study on mass spectroscopy data. J Biomol Struct Dyn 2024:1-10. [PMID: 38285683 DOI: 10.1080/07391102.2024.2310200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 01/19/2024] [Indexed: 01/31/2024]
Abstract
Computational characterization of multiple Histidine (His) post-translational-modifications (PTM) at enzyme active sites complements tedious experimental characterization in proteins-of-unknown-functions (PUFs) and domain-of-unknown-functions (DUFs). There are only a handful of Histidine-PTM-prediction-tools and those also annotate only a single function. Here, we addressed the problem using artificial neural networks on functional histidine dataset curated from enzyme (protein) sequences available in UniProt database (sample size n = 1584). The convolution-neural-network (CNN) model ('Hist-i-fy') performed the best with 75% overall accuracy/F1-score. A case study was performed on histidine-phosphorylation (n = 34) obtained from mass spectroscopy data. For the first time, we report multiple His-PTM-prediction-tool (https://histify.streamlit.app/& https://github.com/dibyansu24-maker/Histify), with optimal performance. The inputs to the tool are (i) protein sequence containing histidine, and (ii) the histidine residue number. Prediction output is one out of the eight histidine functions-acetylation, ribosylation, glycosylation, hydroxylation, methylation, oxidation, phosphorylation, and protein splicing.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Dibyansu Diptiman
- Department of Biological Sciences, Birla Institute of Technology and Science, Hyderabad, India
| | - Abhishek Jalan
- Department of Biological Sciences, Birla Institute of Technology and Science, Hyderabad, India
| | - Rishabh Pal
- Department of Biological Sciences, Birla Institute of Technology and Science, Hyderabad, India
| | - Sachin Dodwani
- Department of Biological Sciences, Birla Institute of Technology and Science, Hyderabad, India
| | - Debashree Bandyopadhyay
- Department of Biological Sciences, Birla Institute of Technology and Science, Hyderabad, India
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3
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Wang Z, Zhang Y, Aweya JJ, Lin Z, Yao D, Zheng Z. The histidine phosphatase LHPP of Penaeus vannamei is involved in shrimp hemocytes apoptosis. FISH AND SHELLFISH IMMUNOLOGY REPORTS 2023; 5:100109. [PMID: 37448875 PMCID: PMC10336261 DOI: 10.1016/j.fsirep.2023.100109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 06/11/2023] [Accepted: 06/26/2023] [Indexed: 07/15/2023] Open
Abstract
LHPP (Phospholysine Phosphohistidine Inorganic Pyrophosphate Phosphatase) is a protein histidine phosphatase that modulates a hidden posttranslational modification called histidine phosphorylation. LHPP also acts as a tumor suppressor, which plays a pivotal role in various cellular processes. However, whether LHPP participates in the regulation of invertebrate's immunity is still unknown. Here we characterized a LHPP homolog in P. vannamei (designated PvLHPP), with a 807 bp length of open reading frame (ORF) encoding a putative protein of 268 amino acids. Sequence analysis revealed that PvLHPP contains a typical hydrolase 6 and hydrolase-like domain, which was conserved from invertebrate to vertebrate. PvLHPP was ubiquitously expressed in tissues and induced in hemocyte and hepatopancreas by Vibrio parahaemolyticus, Streptococcus iniae and white spot syndrome virus (WSSV) challenge, indicating that PvLHPP participated in the immune responses. Moreover, silencing of PvLHPP followed by V. parahaemolyticus inhibited hemocyte apoptosis. This study enriches our current insight on shrimp immunity, and provides novel perspective to understand immune-regulatory role of PvLHPP.
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Affiliation(s)
- Zhongyan Wang
- Institute of Marine Sciences and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, China
| | - Yueling Zhang
- Institute of Marine Sciences and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, China
- STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou 515063, China
| | - Jude Juventus Aweya
- Institute of Marine Sciences and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, China
| | - Zhongyang Lin
- Institute of Marine Sciences and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, China
| | - Defu Yao
- Institute of Marine Sciences and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, China
| | - Zhihong Zheng
- Institute of Marine Sciences and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, China
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Zatorski N, Sun Y, Elmas A, Dallago C, Karl T, Stein D, Rost B, Huang KL, Walsh M, Schlessinger A. Structural Analysis of Genomic and Proteomic Signatures Reveal Dynamic Expression of Intrinsically Disordered Regions in Breast Cancer and Tissue. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.23.529755. [PMID: 36865220 PMCID: PMC9980136 DOI: 10.1101/2023.02.23.529755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/26/2023]
Abstract
Structural features of proteins capture underlying information about protein evolution and function, which enhances the analysis of proteomic and transcriptomic data. Here we develop Structural Analysis of Gene and protein Expression Signatures (SAGES), a method that describes expression data using features calculated from sequence-based prediction methods and 3D structural models. We used SAGES, along with machine learning, to characterize tissues from healthy individuals and those with breast cancer. We analyzed gene expression data from 23 breast cancer patients and genetic mutation data from the COSMIC database as well as 17 breast tumor protein expression profiles. We identified prominent expression of intrinsically disordered regions in breast cancer proteins as well as relationships between drug perturbation signatures and breast cancer disease signatures. Our results suggest that SAGES is generally applicable to describe diverse biological phenomena including disease states and drug effects.
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Affiliation(s)
- Nicole Zatorski
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, One Gustave Levey Pl NY, NY 10029, USA
| | - Yifei Sun
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, One Gustave Levey Pl NY, NY 10029, USA
| | - Abdulkadir Elmas
- Department of Genetic and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave Levey Pl NY, NY 10029, USA
| | - Christian Dallago
- NVIDIA DE GmbH, Einsteinstraße 172, 81677 München, Germany
- Faculty of Informatics, Bioinformatics & Computational Biology, Technical University Munich (TUM), 85748 Garching, Germany
| | - Timothy Karl
- Faculty of Informatics, Bioinformatics & Computational Biology, Technical University Munich (TUM), 85748 Garching, Germany
| | - David Stein
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, One Gustave Levey Pl NY, NY 10029, USA
| | - Burkhard Rost
- Faculty of Informatics, Bioinformatics & Computational Biology, Technical University Munich (TUM), 85748 Garching, Germany
| | - Kuan-Lin Huang
- Department of Genetic and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave Levey Pl NY, NY 10029, USA
| | - Martin Walsh
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, One Gustave Levey Pl NY, NY 10029, USA
| | - Avner Schlessinger
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, One Gustave Levey Pl NY, NY 10029, USA
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Makwana MV, Williamson MP, Jackson RFW, Muimo R. Quantitation of phosphohistidine in proteins in a mammalian cell line by 31P NMR. PLoS One 2022; 17:e0273797. [PMID: 36048825 PMCID: PMC9436146 DOI: 10.1371/journal.pone.0273797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 08/15/2022] [Indexed: 11/23/2022] Open
Abstract
There is growing evidence to suggest that phosphohistidines are present at significant levels in mammalian cells and play a part in regulating cellular activity, in particular signaling pathways related to cancer. Because of the chemical instability of phosphohistidine at neutral or acid pH, it remains unclear how much phosphohistidine is present in cells. Here we describe a protocol for extracting proteins from mammalian cells in a way that avoids loss of covalent phosphates from proteins, and use it to measure phosphohistidine concentrations in human bronchial epithelial cell (16HBE14o-) lysate using 31P NMR spectroscopic analysis. Phosphohistidine is determined on average to be approximately one third as abundant as phosphoserine and phosphothreonine combined (and thus roughly 15 times more abundant than phosphotyrosine). The amount of phosphohistidine, and phosphoserine/phosphothreonine per gram of protein from a cell lysate was determined to be 23 μmol/g and 68 μmol/g respectively. The amount of phosphohistidine, and phosphoserine/phosphothreonine per cell was determined to be 1.8 fmol/cell, and 5.8 fmol/cell respectively. Phosphorylation is largely at the N3 (tele) position. Typical tryptic digest conditions result in loss of most of the phosphohistidine present, which may explain why the amounts reported here are greater than is generally seen using mass spectroscopy assays. The results further strengthen the case for a functional role of phosphohistidine in eukaryotic cells.
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Affiliation(s)
- Mehul V. Makwana
- Department of Chemistry, The University of Sheffield, Sheffield, United Kingdom
- Department of Infection, Immunity and Cardiovascular Disease, The University of Sheffield, Sheffield, United Kingdom
| | - Mike P. Williamson
- School of Biosciences, The University of Sheffield, Sheffield, United Kingdom
| | | | - Richmond Muimo
- Department of Infection, Immunity and Cardiovascular Disease, The University of Sheffield, Sheffield, United Kingdom
- * E-mail:
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Hunter T. A journey from phosphotyrosine to phosphohistidine and beyond. Mol Cell 2022; 82:2190-2200. [PMID: 35654043 DOI: 10.1016/j.molcel.2022.05.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 04/22/2022] [Accepted: 05/05/2022] [Indexed: 10/18/2022]
Abstract
Protein phosphorylation is a reversible post-translational modification. Nine of the 20 natural amino acids in proteins can be phosphorylated, but most of what we know about the roles of protein phosphorylation has come from studies of serine, threonine, and tyrosine phosphorylation. Much less is understood about the phosphorylation of histidine, lysine, arginine, cysteine, aspartate, and glutamate, so-called non-canonical phosphorylations. Phosphohistidine (pHis) was discovered 60 years ago as a mitochondrial enzyme intermediate; since then, evidence for the existence of histidine kinases and phosphohistidine phosphatases has emerged, together with examples where protein function is regulated by reversible histidine phosphorylation. pHis is chemically unstable and has thus been challenging to study. However, the recent development of tools for studying pHis has accelerated our understanding of the multifaceted functions of histidine phosphorylation, revealing a large number of proteins that are phosphorylated on histidine and implicating pHis in a wide range of cellular processes.
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Affiliation(s)
- Tony Hunter
- Molecular Cell Biology, Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
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The many ways that nature has exploited the unusual structural and chemical properties of phosphohistidine for use in proteins. Biochem J 2021; 478:3575-3596. [PMID: 34624072 DOI: 10.1042/bcj20210533] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 09/15/2021] [Accepted: 09/22/2021] [Indexed: 01/12/2023]
Abstract
Histidine phosphorylation is an important and ubiquitous post-translational modification. Histidine undergoes phosphorylation on either of the nitrogens in its imidazole side chain, giving rise to 1- and 3- phosphohistidine (pHis) isomers, each having a phosphoramidate linkage that is labile at high temperatures and low pH, in contrast with stable phosphomonoester protein modifications. While all organisms routinely use pHis as an enzyme intermediate, prokaryotes, lower eukaryotes and plants also use it for signal transduction. However, research to uncover additional roles for pHis in higher eukaryotes is still at a nascent stage. Since the discovery of pHis in 1962, progress in this field has been relatively slow, in part due to a lack of the tools and techniques necessary to study this labile modification. However, in the past ten years the development of phosphoproteomic techniques to detect phosphohistidine (pHis), and methods to synthesize stable pHis analogues, which enabled the development of anti-phosphohistidine (pHis) antibodies, have accelerated our understanding. Recent studies that employed anti-pHis antibodies and other advanced techniques have contributed to a rapid expansion in our knowledge of histidine phosphorylation. In this review, we examine the varied roles of pHis-containing proteins from a chemical and structural perspective, and present an overview of recent developments in pHis proteomics and antibody development.
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