1
|
Sun Z, Ning Z, Figeys D. The Landscape and Perspectives of the Human Gut Metaproteomics. Mol Cell Proteomics 2024; 23:100763. [PMID: 38608842 PMCID: PMC11098955 DOI: 10.1016/j.mcpro.2024.100763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 02/26/2024] [Accepted: 04/09/2024] [Indexed: 04/14/2024] Open
Abstract
The human gut microbiome is closely associated with human health and diseases. Metaproteomics has emerged as a valuable tool for studying the functionality of the gut microbiome by analyzing the entire proteins present in microbial communities. Recent advancements in liquid chromatography and tandem mass spectrometry (LC-MS/MS) techniques have expanded the detection range of metaproteomics. However, the overall coverage of the proteome in metaproteomics is still limited. While metagenomics studies have revealed substantial microbial diversity and functional potential of the human gut microbiome, few studies have summarized and studied the human gut microbiome landscape revealed with metaproteomics. In this article, we present the current landscape of human gut metaproteomics studies by re-analyzing the identification results from 15 published studies. We quantified the limited proteome coverage in metaproteomics and revealed a high proportion of annotation coverage of metaproteomics-identified proteins. We conducted a preliminary comparison between the metaproteomics view and the metagenomics view of the human gut microbiome, identifying key areas of consistency and divergence. Based on the current landscape of human gut metaproteomics, we discuss the feasibility of using metaproteomics to study functionally unknown proteins and propose a whole workflow peptide-centric analysis. Additionally, we suggest enhancing metaproteomics analysis by refining taxonomic classification and calculating confidence scores, as well as developing tools for analyzing the interaction between taxonomy and function.
Collapse
Affiliation(s)
- Zhongzhi Sun
- School of Pharmaceutical Sciences, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada; Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Zhibin Ning
- School of Pharmaceutical Sciences, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Daniel Figeys
- School of Pharmaceutical Sciences, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada; Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada.
| |
Collapse
|
2
|
Malarney KP, Chang PV. Chemoproteomic Approaches for Unraveling Prokaryotic Biology. Isr J Chem 2023; 63:e202200076. [PMID: 37842282 PMCID: PMC10575470 DOI: 10.1002/ijch.202200076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Indexed: 03/07/2023]
Abstract
Bacteria are ubiquitous lifeforms with important roles in the environment, biotechnology, and human health. Many of the functions that bacteria perform are mediated by proteins and enzymes, which catalyze metabolic transformations of small molecules and modifications of proteins. To better understand these biological processes, chemical proteomic approaches, including activity-based protein profiling, have been developed to interrogate protein function and enzymatic activity in physiologically relevant contexts. Here, chemoproteomic strategies and technological advances for studying bacterial physiology, pathogenesis, and metabolism are discussed. The development of chemoproteomic approaches for characterizing protein function and enzymatic activity within bacteria remains an active area of research, and continued innovations are expected to provide breakthroughs in understanding bacterial biology.
Collapse
Affiliation(s)
- Kien P Malarney
- Department of Microbiology, Cornell University, Ithaca, NY 14853 (USA)
| | - Pamela V Chang
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14853 (USA)
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853 (USA)
- Cornell Center for Immunology, Cornell University, Ithaca, NY 14853 (USA)
- Cornell Institute of Host-Microbe Interactions and Disease, Cornell University, Ithaca, NY 14853 (USA)
| |
Collapse
|
3
|
Ramanathan R, Hatzios SK. Activity-based Tools for Interrogating Host Biology During Infection. Isr J Chem 2023; 63:e202200095. [PMID: 37744997 PMCID: PMC10512441 DOI: 10.1002/ijch.202200095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Indexed: 02/18/2023]
Abstract
Host cells sense and respond to pathogens by dynamically regulating cell signaling. The rapid modulation of signaling pathways is achieved by post-translational modifications (PTMs) that can alter protein structure, function, and/or binding interactions. By using chemical probes to broadly profile changes in enzyme function or side-chain reactivity, activity-based protein profiling (ABPP) can reveal PTMs that regulate host-microbe interactions. While ABPP has been widely utilized to uncover microbial mechanisms of pathogenesis, in this review, we focus on more recent applications of this technique to the discovery of host PTMs and enzymes that modulate signaling within infected cells. Collectively, these advances underscore the importance of ABPP as a tool for interrogating the host response to infection and identifying potential targets for host-directed therapies.
Collapse
Affiliation(s)
- Renuka Ramanathan
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520 USA
- Microbial Sciences Institute, Yale University, West Haven, CT 06516 USA
| | - Stavroula K. Hatzios
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520 USA
- Microbial Sciences Institute, Yale University, West Haven, CT 06516 USA
- Department of Chemistry, Yale University, New Haven, CT 06520 USA
| |
Collapse
|
4
|
Kleiner M, Kouris A, Violette M, D'Angelo G, Liu Y, Korenek A, Tolić N, Sachsenberg T, McCalder J, Lipton MS, Strous M. Ultra-sensitive isotope probing to quantify activity and substrate assimilation in microbiomes. Microbiome 2023; 11:24. [PMID: 36755313 PMCID: PMC9909930 DOI: 10.1186/s40168-022-01454-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 12/20/2022] [Indexed: 06/18/2023]
Abstract
BACKGROUND Stable isotope probing (SIP) approaches are a critical tool in microbiome research to determine associations between species and substrates, as well as the activity of species. The application of these approaches ranges from studying microbial communities important for global biogeochemical cycling to host-microbiota interactions in the intestinal tract. Current SIP approaches, such as DNA-SIP or nanoSIMS allow to analyze incorporation of stable isotopes with high coverage of taxa in a community and at the single cell level, respectively, however they are limited in terms of sensitivity, resolution or throughput. RESULTS Here, we present an ultra-sensitive, high-throughput protein-based stable isotope probing approach (Protein-SIP), which cuts cost for labeled substrates by 50-99% as compared to other SIP and Protein-SIP approaches and thus enables isotope labeling experiments on much larger scales and with higher replication. The approach allows for the determination of isotope incorporation into microbiome members with species level resolution using standard metaproteomics liquid chromatography-tandem mass spectrometry (LC-MS/MS) measurements. At the core of the approach are new algorithms to analyze the data, which have been implemented in an open-source software ( https://sourceforge.net/projects/calis-p/ ). We demonstrate sensitivity, precision and accuracy using bacterial cultures and mock communities with different labeling schemes. Furthermore, we benchmark our approach against two existing Protein-SIP approaches and show that in the low labeling range used our approach is the most sensitive and accurate. Finally, we measure translational activity using 18O heavy water labeling in a 63-species community derived from human fecal samples grown on media simulating two different diets. Activity could be quantified on average for 27 species per sample, with 9 species showing significantly higher activity on a high protein diet, as compared to a high fiber diet. Surprisingly, among the species with increased activity on high protein were several Bacteroides species known as fiber consumers. Apparently, protein supply is a critical consideration when assessing growth of intestinal microbes on fiber, including fiber-based prebiotics. CONCLUSIONS We demonstrate that our Protein-SIP approach allows for the ultra-sensitive (0.01 to 10% label) detection of stable isotopes of elements found in proteins, using standard metaproteomics data.
Collapse
Affiliation(s)
- Manuel Kleiner
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, USA.
| | - Angela Kouris
- Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - Marlene Violette
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, USA
| | - Grace D'Angelo
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, USA
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Yihua Liu
- Department of Geoscience, University of Calgary, Calgary, AB, Canada
- Max Planck Institute for Biology, Tübingen, Germany
| | - Abigail Korenek
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, USA
| | - Nikola Tolić
- Environmental Molecular Science Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Timo Sachsenberg
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen, Germany
| | - Janine McCalder
- Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - Mary S Lipton
- Environmental Molecular Science Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Marc Strous
- Department of Geoscience, University of Calgary, Calgary, AB, Canada.
| |
Collapse
|
5
|
Canderan J, Stamboulian M, Ye Y. MetaProD: A Highly-Configurable Mass Spectrometry Analyzer for Multiplexed Proteomic and Metaproteomic Data. J Proteome Res 2023; 22:442-453. [PMID: 36688801 PMCID: PMC9903327 DOI: 10.1021/acs.jproteome.2c00614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Indexed: 01/24/2023]
Abstract
The microbiome has been shown to be important for human health because of its influence on disease and the immune response. Mass spectrometry is an important tool for evaluating protein expression and species composition in the microbiome but is technically challenging and time-consuming. Multiplexing has emerged as a way to make spectrometry workflows faster while improving results. Here, we present MetaProD (MetaProteomics in Django) as a highly configurable metaproteomic data analysis pipeline supporting label-free and multiplexed mass spectrometry. The pipeline is open-source, uses fully open-source tools, and is integrated with Django to offer a web-based interface for configuration and data access. Benchmarking of MetaProD using multiple metaproteomics data sets showed that MetaProD achieved fast and efficient identification of peptides and proteins. Application of MetaProD to a multiplexed cancer data set resulted in identification of more differentially expressed human proteins in cancer tissues versus healthy tissues as compared to previous studies; in addition, MetaProD identified bacterial proteins in those samples, some of which are differentially abundant.
Collapse
Affiliation(s)
- Jamie Canderan
- Informatics
Department, Luddy School of Informatics, Computing and Engineering, Indiana University, Bloomington, Indiana 47408, United States
| | - Moses Stamboulian
- Informatics
Department, Luddy School of Informatics, Computing and Engineering, Indiana University, Bloomington, Indiana 47408, United States
| | - Yuzhen Ye
- Computer
Science Department, Luddy School of Informatics, Computing and Engineering, Indiana University, Bloomington, Indiana 47408, United States
| |
Collapse
|
6
|
Saralegui C, García-Durán C, Romeu E, Hernáez-Sánchez ML, Maruri A, Bastón-Paz N, Lamas A, Vicente S, Pérez-Ruiz E, Delgado I, Luna-Paredes C, Caballero JDD, Zamora J, Monteoliva L, Gil C, del Campo R. Statistical Evaluation of Metaproteomics and 16S rRNA Amplicon Sequencing Techniques for Study of Gut Microbiota Establishment in Infants with Cystic Fibrosis. Microbiol Spectr 2022; 10:e0146622. [PMID: 36255300 PMCID: PMC9784762 DOI: 10.1128/spectrum.01466-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 09/23/2022] [Indexed: 01/05/2023] Open
Abstract
Newborn screening for cystic fibrosis (CF) can identify affected but asymptomatic infants. The selection of omic technique for gut microbiota study is crucial due to both the small amount of feces available and the low microorganism load. Our aims were to compare the agreement between 16S rRNA amplicon sequencing and metaproteomics by a robust statistical analysis, including both presence and abundance of taxa, to describe the sequential establishment of the gut microbiota during the first year of life in a small size sample (8 infants and 28 fecal samples). The taxonomic assignations by the two techniques were similar, whereas certain discrepancies were observed in the abundance detection, mostly the lower predicted relative abundance of Bifidobacterium and the higher predicted relative abundance of certain Firmicutes and Proteobacteria by amplicon sequencing. During the first months of life, the CF gut microbiota is characterized by a significant enrichment of Ruminococcus gnavus, the expression of certain virulent bacterial traits, and the detection of human inflammation-related proteins. Metaproteomics provides information on composition and functionality, as well as data on host-microbiome interactions. Its strength is the identification and quantification of Actinobacteria and certain classes of Firmicutes, but alpha diversity indices are not comparable to those of amplicon sequencing. Both techniques detected an aberrant microbiota in our small cohort of infants with CF during their first year of life, dominated by the enrichment of R. gnavus within a human inflammatory environment. IMPORTANCE In recent years, some techniques have been incorporated for the study of microbial ecosystems, being 16S rRNA gene sequencing being the most widely used. Metaproteomics provides the advantage of identifying the interaction between microorganisms and human cells, but the available databases are less extensive as well as imprecise. Few studies compare the statistical differences between the two techniques to define the composition of an ecosystem. Our work shows that the two methods are comparable in terms of microorganism identification but provide different results in alpha diversity analysis. On the other hand, we have studied newborns with cystic fibrosis, for whom we have described the establishment of an intestinal ecosystem marked by the inflammatory response of the host and the enrichment of Ruminococcus gnavus.
Collapse
Affiliation(s)
- Claudia Saralegui
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
- CIBERINFEC, Madrid, Spain
- Unidad de Fibrosis Quística, Hospital Universitario Ramón y Cajal, Madrid, Spain
| | - Carmen García-Durán
- Departamento de Microbiología y Parasitología, Universidad Complutense de Madrid and Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
| | - Eduardo Romeu
- Unidad de Proteómica, Universidad Complutense de Madrid, Madrid, Spain
| | | | - Ainhize Maruri
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
- CIBERINFEC, Madrid, Spain
- Unidad de Fibrosis Quística, Hospital Universitario Ramón y Cajal, Madrid, Spain
| | - Natalia Bastón-Paz
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
- CIBERINFEC, Madrid, Spain
- Unidad de Fibrosis Quística, Hospital Universitario Ramón y Cajal, Madrid, Spain
| | - Adelaida Lamas
- Unidad de Fibrosis Quística, Hospital Universitario Ramón y Cajal, Madrid, Spain
- Servicio de Pediatría, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
| | - Saioa Vicente
- Unidad de Fibrosis Quística, Hospital Universitario Ramón y Cajal, Madrid, Spain
- Servicio de Pediatría, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
| | - Estela Pérez-Ruiz
- Unidad de Fibrosis Quística, Hospital Regional Universitario de Málaga, Málaga, Spain
| | - Isabel Delgado
- Unidad de Fibrosis Quística, Hospital Virgen del Rocío, Seville, Spain
| | - Carmen Luna-Paredes
- Sección de Neumología y Alergia Infantil, Unidad Multidisciplinar Fibrosis Quística, Hospital Doce de Octubre, Madrid, Spain
| | - Juan de Dios Caballero
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
- CIBERINFEC, Madrid, Spain
- Unidad de Fibrosis Quística, Hospital Universitario Ramón y Cajal, Madrid, Spain
| | - Javier Zamora
- Unidad de Bioestadística, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria and CIBERESP, Madrid, Spain
| | - Lucía Monteoliva
- Departamento de Microbiología y Parasitología, Universidad Complutense de Madrid and Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
- Unidad de Proteómica, Universidad Complutense de Madrid, Madrid, Spain
| | - Concepción Gil
- Departamento de Microbiología y Parasitología, Universidad Complutense de Madrid and Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
- Unidad de Proteómica, Universidad Complutense de Madrid, Madrid, Spain
| | - Rosa del Campo
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
- CIBERINFEC, Madrid, Spain
- Unidad de Fibrosis Quística, Hospital Universitario Ramón y Cajal, Madrid, Spain
- Universidad Alfonso X El Sabio, Madrid, Spain
| |
Collapse
|
7
|
Wang T, Yu R, Zhu L, Wang X, Yang B. Differences in the Intestinal Flora of Patients with Inflammatory Bowel Disease in Southwest China. Indian J Microbiol 2022; 62:384-392. [PMID: 35974916 PMCID: PMC9375786 DOI: 10.1007/s12088-022-01014-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 03/05/2022] [Indexed: 11/27/2022] Open
Abstract
To study changes in the intestinal flora associated with inflammatory bowel disease (IBD) in the Han population of southwest China, 48 participants were enrolled, 18 of whom had been diagnosed with IBD. Stool samples were collected from the participants. Sequencing of 16S rRNA gene was used to measure and identify the components of the intestinal flora. Diversity analysis and multivariate statistical analysis were conducted to study differences in intestinal flora between patients with IBD and healthy controls. The goods coverage, observed species, Shannon, and Simpson indices of alpha diversity were different (p < 0.05). Beta diversity analysis yielded significant differences between groups (R = 0.5668, p = 0.001 < 0.05). Compared with the composition of the intestinal flora in healthy controls, the relative abundances of Proteobacteria (18.56% vs. 3.56%, p = 0.001) and Fusobacterium (2.08% vs. 0.35%, p = 0.005) were higher in patients with IBD. Therefore, this study provides insight into the role of the microbiome in IBD. Supplementary Information The online version contains supplementary material available at 10.1007/s12088-022-01014-z.
Collapse
Affiliation(s)
- Tingting Wang
- Department of Laboratory Medicine, West China Hospital of Sichuan University, Chengdu, China
| | - Renlin Yu
- Department of Clinical Laboratory, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Lingling Zhu
- Department of Laboratory Medicine, West China Hospital of Sichuan University, Chengdu, China
| | - Xuean Wang
- Department of Laboratory Medicine, West China Hospital of Sichuan University, Chengdu, China
| | - Bin Yang
- Department of Laboratory Medicine, West China Hospital of Sichuan University, Chengdu, China
| |
Collapse
|
8
|
Decraecker L, Boeckxstaens G, Denadai-Souza A. Inhibition of Serine Proteases as a Novel Therapeutic Strategy for Abdominal Pain in IBS. Front Physiol 2022; 13:880422. [PMID: 35665224 PMCID: PMC9161638 DOI: 10.3389/fphys.2022.880422] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 04/26/2022] [Indexed: 02/06/2023] Open
Abstract
Serine proteases are heavily present in the gastrointestinal tract where they are essential in numerous physiological processes. An imbalance in the proteolytic activity is a central mechanism underlying abdominal pain in irritable bowel syndrome (IBS). Therefore, protease inhibitors are emerging as a promising therapeutic tool to manage abdominal pain in this functional gastrointestinal disorder. With this review, we provide an up-to-date overview of the implications of serine proteases in the development of abdominal pain in IBS, along with a critical assessment of the current developments and prospects of protease inhibitors as a therapeutic tool. In particular, we highlight the current knowledge gap concerning the identity of dysregulated serine proteases that are released by the rectal mucosa of IBS patients. Finally, we suggest a workflow with state-of-the-art techniques that will help address the knowledge gap, guiding future research towards the development of more effective and selective protease inhibitors to manage abdominal pain in IBS.
Collapse
|
9
|
Miranda RR, Parthasarathy A, Hudson AO. Exploration of Chemical Biology Approaches to Facilitate the Discovery and Development of Novel Antibiotics. Front Trop Dis 2022. [DOI: 10.3389/fitd.2022.845469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Approximately 2.8 million people worldwide are infected with bacteria that are deemed resistant to clinically relevant antibiotics. This accounts for 700,000 deaths every year and represents a major public health threat that has been on the rise for the past two decades. In contrast, the pace of antibiotic discovery to treat these resistant pathogens has significantly decreased. Most antibiotics are complex natural products that were isolated from soil microorganisms during the golden era of antibiotic discovery (1940s to 1960s) employing the “Waksman platform”. After the collapse of this discovery platform, other strategies and approaches emerged, including phenotype- or target-based screenings of large synthetic compound libraries. However, these methods have not resulted in the discovery and/or development of new drugs for clinical use in over 30 years. A better understanding of the structure and function of the molecular components that constitute the bacterial system is of paramount importance to design new strategies to tackle drug-resistant pathogens. Herein, we review the traditional approaches as well as novel strategies to facilitate antibiotic discovery that are chemical biology-focused. These include the design and application of chemical probes that can undergo bioorthogonal reactions, such as copper (I)-catalyzed azide-alkyne cycloadditions (CuAAC). By specifically interacting with bacterial proteins or being incorporated in the microorganism’s metabolism, chemical probes are powerful tools in drug discovery that can help uncover new drug targets and investigate the mechanisms of action and resistance of new antibacterial leads.
Collapse
|
10
|
Levi Mortera S, Vernocchi P, Basadonne I, Zandonà A, Chierici M, Durighello M, Marzano V, Gardini S, Gasbarrini A, Urbani A, Vicari S, Roncada P, Furlanello C, Venuti P, Putignani L. A metaproteomic-based gut microbiota profiling in children affected by autism spectrum disorders. J Proteomics 2022; 251:104407. [PMID: 34763095 DOI: 10.1016/j.jprot.2021.104407] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 09/02/2021] [Accepted: 10/13/2021] [Indexed: 12/15/2022]
Abstract
During the last decade, the evidences on the relationship between neurodevelopmental disorders and the microbial communities of the intestinal tract have considerably grown. Particularly, the role of gut microbiota (GM) ecology and predicted functions in Autism Spectrum Disorders (ASD) has been especially investigated by 16S rRNA targeted and shotgun metagenomics, trying to assess disease signature and their correlation with cognitive impairment or gastrointestinal (GI) manifestations of the disease. Herein we present a metaproteomic approach to point out the microbial gene expression profiles, their functional annotations, and the taxonomic distribution of gut microbial communities in ASD children. We pursued a LC-MS/MS based investigation, to compare the GM profiles of patients with those of their respective relatives and aged-matched controls, providing a quantitative evaluation of bacterial metaproteins by SWATH analysis. All data were managed by a multiple step bioinformatic pipeline, including network analysis. In particular, comparing ASD subjects with CTRLs, up-regulation was found for some metaproteins associated with Clostridia and with carbohydrate metabolism (glyceraldehyde-3-phosphate and glutamate dehydrogenases), while down-regulation was observed for others associated with Bacteroidia (SusC and SusD family together with the TonB dependent receptor). Moreover, network analysis highlighted specific microbial correlations among ASD subgroups characterized by different functioning levels and GI symptoms. SIGNIFICANCE: To the best of our knowledge, this study represents the first metaproteomic investigation on the gut microbiota of ASD children compared with relatives and age-matched CTRLs. Remarkably, the applied SWATH methodology allowed the attribution of differentially regulated functions to specific microbial taxa, offering a novel and complementary point of view with respect to previous studies.
Collapse
Affiliation(s)
- Stefano Levi Mortera
- Multimodal Laboratory Medicine Research Area, Unit of Human Microbiome, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Pamela Vernocchi
- Multimodal Laboratory Medicine Research Area, Unit of Human Microbiome, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Ilaria Basadonne
- Department of Psychology and Cognitive Sciences, University of Trento, Rovereto, Italy
| | | | | | - Martina Durighello
- Multimodal Laboratory Medicine Research Area, Unit of Human Microbiome, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Valeria Marzano
- Multimodal Laboratory Medicine Research Area, Unit of Human Microbiome, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | | | - Antonio Gasbarrini
- Istituto di Patologia Speciale Medica, Università Cattolica del Sacro Cuore, Rome, Italy; UOC Medicina Interna e Gastroenterologia, Area Gastroenterologia ed Oncologia Medica, Dipartimento di Scienze Gastroenterologiche, Endocrino-Metaboliche e Nefro-Urologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Andrea Urbani
- Clinical Chemistry, Biochemistry and Molecular Biology Operations (UOC), Agostino Gemelli Foundation University Hospital IRCCS, Rome, Italy; Department of Basic Biotechnological Sciences, Intensivological and Perioperative Clinics, Catholic University of Sacred Heart, Rome, Italy
| | - Stefano Vicari
- Department of Neuroscience, Unit of Head Child & Adolescent Psychiatry, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy; Department of Life Sciences and Public Health, Catholic University of Sacred Heart, Rome, Italy
| | - Paola Roncada
- Department of Health Sciences, University 'Magna Græcia' of Catanzaro, Catanzaro, Italy
| | | | - Paola Venuti
- Department of Psychology and Cognitive Sciences, University of Trento, Rovereto, Italy
| | - Lorenza Putignani
- Department of Diagnostics and Laboratory Medicine, Unit of Microbiology and Diagnostic Immunology, Unit of Microbiomics and Multimodal Laboratory Medicine Research Area, Unit of Human Microbiome, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy.
| |
Collapse
|
11
|
Thuy-Boun PS, Wang AY, Crissien-Martinez A, Xu JH, Chatterjee S, Stupp GS, Su AI, Coyle WJ, Wolan DW. Quantitative metaproteomics and activity-based protein profiling of patient fecal microbiome identifies host and microbial serine-type endopeptidase activity associated with ulcerative colitis. Mol Cell Proteomics 2022; 21:100197. [PMID: 35033677 PMCID: PMC8941213 DOI: 10.1016/j.mcpro.2022.100197] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 01/10/2022] [Accepted: 01/11/2022] [Indexed: 12/12/2022] Open
Abstract
The gut microbiota plays an important yet incompletely understood role in the induction and propagation of ulcerative colitis (UC). Organism-level efforts to identify UC-associated microbes have revealed the importance of community structure, but less is known about the molecular effectors of disease. We performed 16S rRNA gene sequencing in parallel with label-free data-dependent LC-MS/MS proteomics to characterize the stool microbiomes of healthy (n = 8) and UC (n = 10) patients. Comparisons of taxonomic composition between techniques revealed major differences in community structure partially attributable to the additional detection of host, fungal, viral, and food peptides by metaproteomics. Differential expression analysis of metaproteomic data identified 176 significantly enriched protein groups between healthy and UC patients. Gene ontology analysis revealed several enriched functions with serine-type endopeptidase activity overrepresented in UC patients. Using a biotinylated fluorophosphonate probe and streptavidin-based enrichment, we show that serine endopeptidases are active in patient fecal samples and that additional putative serine hydrolases are detectable by this approach compared with unenriched profiling. Finally, as metaproteomic databases expand, they are expected to asymptotically approach completeness. Using ComPIL and de novo peptide sequencing, we estimate the size of the probable peptide space unidentified (“dark peptidome”) by our large database approach to establish a rough benchmark for database sufficiency. Despite high variability inherent in patient samples, our analysis yielded a catalog of differentially enriched proteins between healthy and UC fecal proteomes. This catalog provides a clinically relevant jumping-off point for further molecular-level studies aimed at identifying the microbial underpinnings of UC. Identified 176 significantly altered protein groups between healthy and UC patients. Serine-type endopeptidase activity is overrepresented in UC patients. Fluorophosphonate ABPP shows that endopeptidases are active in fecal samples. ABPP enrichment helps identify additional putative serine hydrolases in samples. De novo sequencing used to estimate number of MS2 spectra unidentified by ComPIL.
Collapse
Affiliation(s)
- Peter S Thuy-Boun
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037
| | - Ana Y Wang
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037
| | | | - Janice H Xu
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037
| | - Sandip Chatterjee
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037
| | - Gregory S Stupp
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037
| | - Andrew I Su
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037
| | - Walter J Coyle
- Scripps Clinic Gastroenterology Division, La Jolla, CA 92037
| | - Dennis W Wolan
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037.
| |
Collapse
|
12
|
Boeri L, Donnaloja F, Campanile M, Sardelli L, Tunesi M, Fusco F, Giordano C, Albani D. Using integrated meta-omics to appreciate the role of the gut microbiota in epilepsy. Neurobiol Dis 2022; 164:105614. [PMID: 35017031 DOI: 10.1016/j.nbd.2022.105614] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 12/31/2021] [Accepted: 01/05/2022] [Indexed: 12/16/2022] Open
Abstract
The way the human microbiota may modulate neurological pathologies is a fascinating matter of research. Epilepsy is a common neurological disorder, which has been largely investigated in correlation with microbiota health and function. However, the mechanisms that regulate this apparent connection are scarcely defined, and extensive effort has been conducted to understand the role of microbiota in preventing and reducing epileptic seizures. Intestinal bacteria seem to modulate the seizure frequency mainly by releasing neurotransmitters and inflammatory mediators. In order to elucidate the complex microbial contribution to epilepsy pathophysiology, integrated meta-omics could be pivotal. In fact, the combination of two or more meta-omics approaches allows a multifactorial study of microbial activity within the frame of disease or drug treatments. In this review, we provide information depicting and supporting the use of multi-omics to study the microbiota-epilepsy connection. We described different meta-omics analyses (metagenomics, metatranscriptomics, metaproteomics and metabolomics), focusing on current technical challenges in stool collection procedures, sample extraction methods and data processing. We further discussed the current advantages and limitations of using the integrative approach of multi-omics in epilepsy investigations.
Collapse
Affiliation(s)
- Lucia Boeri
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milan, Italy.
| | - Francesca Donnaloja
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milan, Italy.
| | - Marzia Campanile
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milan, Italy.
| | - Lorenzo Sardelli
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milan, Italy.
| | - Marta Tunesi
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milan, Italy.
| | - Federica Fusco
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milan, Italy.
| | - Carmen Giordano
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milan, Italy.
| | - Diego Albani
- Department of Neuroscience, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, via Mario Negri 2, 20156 Milan, Italy.
| |
Collapse
|
13
|
Simopoulos CMA, Figeys D, Lavallée-Adam M. Novel Bioinformatics Strategies Driving Dynamic Metaproteomic Studies. Methods Mol Biol 2022; 2456:319-338. [PMID: 35612752 DOI: 10.1007/978-1-0716-2124-0_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Constant improvements in mass spectrometry technologies and laboratory workflows have enabled the proteomics investigation of biological samples of growing complexity. Microbiomes represent such complex samples for which metaproteomics analyses are becoming increasingly popular. Metaproteomics experimental procedures create large amounts of data from which biologically relevant signal must be efficiently extracted to draw meaningful conclusions. Such a data processing requires appropriate bioinformatics tools specifically developed for, or capable of handling metaproteomics data. In this chapter, we outline current and novel tools that can perform the most commonly used steps in the analysis of cutting-edge metaproteomics data, such as peptide and protein identification and quantification, as well as data normalization, imputation, mining, and visualization. We also provide details about the experimental setups in which these tools should be used.
Collapse
Affiliation(s)
- Caitlin M A Simopoulos
- Department of Biochemistry, Microbiology and Immunology and Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON, Canada
| | - Daniel Figeys
- Department of Biochemistry, Microbiology and Immunology and Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON, Canada
- School of Pharmaceutical Sciences, University of Ottawa, Ottawa, ON, Canada
| | - Mathieu Lavallée-Adam
- Department of Biochemistry, Microbiology and Immunology and Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON, Canada.
| |
Collapse
|
14
|
Taguer M, Darbinian E, Wark K, Ter-Cheam A, Stephens DA, Maurice CF. Changes in Gut Bacterial Translation Occur before Symptom Onset and Dysbiosis in Dextran Sodium Sulfate-Induced Murine Colitis. mSystems 2021; 6:e0050721. [PMID: 34874778 PMCID: PMC8651081 DOI: 10.1128/msystems.00507-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 10/20/2021] [Indexed: 11/30/2022] Open
Abstract
Longitudinal studies on the gut microbiome that follow the effect of a perturbation are critical in understanding the microbiome's response and succession to disease. Here, we use a dextran sodium sulfate (DSS) mouse model of colitis as a tractable perturbation to study how gut bacteria change their physiology over the course of a perturbation. Using single-cell methods such as flow cytometry, bioorthogonal noncanonical amino acid tagging (BONCAT), and population-based cell sorting combined with 16S rRNA sequencing, we determine the diversity of physiologically distinct fractions of the gut microbiota and how they respond to a controlled perturbation. The physiological markers of bacterial activity studied here include relative nucleic acid content, membrane damage, and protein production. There is a distinct and reproducible succession in bacterial physiology, with an increase in bacteria with membrane damage and diversity changes in the translationally active fraction, both, critically, occurring before symptom onset. Large increases in the relative abundance of Akkermansia were seen in all physiological fractions, most notably in the translationally active bacteria. Performing these analyses within a detailed, longitudinal framework determines which bacteria change their physiology early on, focusing therapeutic efforts in the future to predict or even mitigate relapse in diseases like inflammatory bowel diseases. IMPORTANCE Most studies on the gut microbiome focus on the composition of this community and how it changes in disease. However, how the community transitions from a healthy state to one associated with disease is currently unknown. Additionally, common diversity metrics do not provide functional information on bacterial activity. We begin to address these two unknowns by following bacterial activity over the course of disease progression, using a tractable mouse model of colitis. We find reproducible changes in gut bacterial physiology that occur before symptom onset, with increases in the proportion of bacteria with membrane damage, and changes in community composition of the translationally active bacteria. Our data provide a framework to identify possible windows of intervention and which bacteria to target in microbiome-based therapeutics.
Collapse
Affiliation(s)
- M. Taguer
- Department of Microbiology & Immunology, Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec, Canada
| | - E. Darbinian
- Department of Microbiology & Immunology, Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec, Canada
| | - K. Wark
- Department of Microbiology & Immunology, Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec, Canada
| | - A. Ter-Cheam
- Department of Mathematics and Statistics, Faculty of Science, McGill University, Montreal, Quebec, Canada
| | - D. A. Stephens
- Department of Mathematics and Statistics, Faculty of Science, McGill University, Montreal, Quebec, Canada
| | - C. F. Maurice
- Department of Microbiology & Immunology, Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec, Canada
| |
Collapse
|
15
|
Pettersen VK, Antunes LCM, Dufour A, Arrieta MC. Inferring early-life host and microbiome functions by mass spectrometry-based metaproteomics and metabolomics. Comput Struct Biotechnol J 2021; 20:274-286. [PMID: 35024099 PMCID: PMC8718658 DOI: 10.1016/j.csbj.2021.12.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 12/08/2021] [Accepted: 12/08/2021] [Indexed: 12/17/2022] Open
Abstract
Humans have a long-standing coexistence with microorganisms. In particular, the microbial community that populates the human gastrointestinal tract has emerged as a critical player in governing human health and disease. DNA and RNA sequencing techniques that map taxonomical composition and genomic potential of the gut community have become invaluable for microbiome research. However, deriving a biochemical understanding of how activities of the gut microbiome shape host development and physiology requires an expanded experimental design that goes beyond these approaches. In this review, we explore advances in high-throughput techniques based on liquid chromatography-mass spectrometry. These omics methods for the identification of proteins and metabolites have enabled direct characterisation of gut microbiome functions and the crosstalk with the host. We discuss current metaproteomics and metabolomics workflows for producing functional profiles, the existing methodological challenges and limitations, and recent studies utilising these techniques with a special focus on early life gut microbiome.
Collapse
Affiliation(s)
- Veronika Kuchařová Pettersen
- Research Group for Host-Microbe Interactions, Department of Medical Biology, UiT The Arctic University of Norway, Tromsø, Norway
- Pediatric Research Group, Department of Clinical Medicine, UiT The Arctic University of Norway, Tromsø, Norway
- Centre for New Antibacterial Strategies, UiT The Arctic University of Norway, Tromsø, Norway
| | - Luis Caetano Martha Antunes
- Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, Brazil
- National Institute of Science and Technology of Innovation on Diseases of Neglected Populations, Center for Technological Development in Health, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, Brazil
| | - Antoine Dufour
- Department of Physiology & Pharmacology, University of Calgary, Calgary, Canada
| | - Marie-Claire Arrieta
- Department of Physiology & Pharmacology, University of Calgary, Calgary, Canada
- Department of Pediatrics, University of Calgary, Calgary, AB, Canada
- International Microbiome Centre, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| |
Collapse
|
16
|
Abstract
Recent advances have identified significant associations between the composition and function of the gut microbiota and various disorders in organ systems other than the digestive tract. Utilizing next-generation sequencing and multiomics approaches, the microbial community that possibly impacts ocular disease has been identified. This review provides an overview of the literature on approaches to microbiota analysis and the roles of commensal microbes in ophthalmic diseases, including autoimmune uveitis, age-related macular degeneration, glaucoma, and other ocular disorders. In addition, this review discusses the hypothesis of the "gut-eye axis" and evaluates the therapeutic potential of targeting commensal microbiota to alleviate ocular inflammation.
Collapse
Affiliation(s)
- Wei Xue
- State Key Laboratory of Ophthalmology, Sun Yat-sen University, Guangzhou, China
| | - Jing Jing Li
- State Key Laboratory of Ophthalmology, Sun Yat-sen University, Guangzhou, China
| | - Yanli Zou
- State Key Laboratory of Ophthalmology, Sun Yat-sen University, Guangzhou, China.,Department of Ophthalmology, Affiliated Foshan Hospital, Southern Medical University, Foshan, China
| | - Bin Zou
- State Key Laboratory of Ophthalmology, Sun Yat-sen University, Guangzhou, China
| | - Lai Wei
- State Key Laboratory of Ophthalmology, Sun Yat-sen University, Guangzhou, China
| |
Collapse
|
17
|
Montenegro-Burke JR, Kok BP, Guijas C, Domingo-Almenara X, Moon C, Galmozzi A, Kitamura S, Eckmann L, Saez E, Siuzdak GE, Wolan DW. Metabolomics activity screening of T cell-induced colitis reveals anti-inflammatory metabolites. Sci Signal 2021; 14:eabf6584. [PMID: 34582249 DOI: 10.1126/scisignal.abf6584] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
[Figure: see text].
Collapse
Affiliation(s)
- J Rafael Montenegro-Burke
- Scripps Center for Metabolomics and Mass Spectrometry, Scripps Research Institute; La Jolla, California 92037, USA
| | - Bernard P Kok
- Scripps Center for Metabolomics and Mass Spectrometry, Scripps Research Institute; La Jolla, California 92037, USA
| | - Carlos Guijas
- Scripps Center for Metabolomics and Mass Spectrometry, Scripps Research Institute; La Jolla, California 92037, USA
| | - Xavier Domingo-Almenara
- Scripps Center for Metabolomics and Mass Spectrometry, Scripps Research Institute; La Jolla, California 92037, USA
| | - Clara Moon
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Andrea Galmozzi
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Seiya Kitamura
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Lars Eckmann
- Department of Medicine, University of California, La Jolla CA 92093, USA
| | - Enrique Saez
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Gary E Siuzdak
- Scripps Center for Metabolomics and Mass Spectrometry, Scripps Research Institute; La Jolla, California 92037, USA.,Department of Structural and Computational Biology, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Dennis W Wolan
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037, USA.,Department of Structural and Computational Biology, Scripps Research Institute, La Jolla, CA 92037, USA
| |
Collapse
|
18
|
Abstract
All living organisms depend on tightly regulated cellular networks to control biological functions. Proteolysis is an important irreversible post-translational modification that regulates most, if not all, cellular processes. Proteases are a large family of enzymes that perform hydrolysis of protein substrates, leading to protein activation or degradation. The 473 known and 90 putative human proteases are divided into 5 main mechanistic groups: metalloproteases, serine proteases, cysteine proteases, threonine proteases, and aspartic acid proteases. Proteases are fundamental to all biological systems, and when dysregulated they profoundly influence disease progression. Inhibiting proteases has led to effective therapies for viral infections, cardiovascular disorders, and blood coagulation just to name a few. Between 5 and 10% of all pharmaceutical targets are proteases, despite limited knowledge about their biological roles. More than 50% of all human proteases have no known substrates. We present here a comprehensive list of all current known human proteases. We also present current and novel biochemical tools to characterize protease functions in vitro, in vivo, and ex vivo. These tools make it achievable to define both beneficial and detrimental activities of proteases in health and disease.
Collapse
Affiliation(s)
- Longxiang Wang
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Kimberly Main
- Department of Physiology & Pharmacology, University of Calgary, Calgary, AB T2N 1N4, Canada.,McCaig Institute for Bone & Joint Health, University of Calgary, Calgary, AB T2N 1N4, Canada.,Hotchkiss Brain Institute, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Henry Wang
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Olivier Julien
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Antoine Dufour
- Department of Physiology & Pharmacology, University of Calgary, Calgary, AB T2N 1N4, Canada.,McCaig Institute for Bone & Joint Health, University of Calgary, Calgary, AB T2N 1N4, Canada.,Hotchkiss Brain Institute, University of Calgary, Calgary, AB T2N 1N4, Canada
| |
Collapse
|
19
|
Takamura A, Thuy-Boun PS, Kitamura S, Han Z, Wolan DW. A photoaffinity probe that targets folate-binding proteins. Bioorg Med Chem Lett 2021; 40:127903. [PMID: 33713779 DOI: 10.1016/j.bmcl.2021.127903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 01/25/2021] [Accepted: 02/15/2021] [Indexed: 11/16/2022]
Abstract
Folate and related derivatives are essential small molecules required for survival. Of significant interest is the biological role and necessity of folate in the crosstalk between commensal organisms and their respective hosts, including the tremendously complex human distal gut microbiome. Here, we designed a folate-based probe consisting of a photo-crosslinker to detect and quantitate folate-binding proteins from proteomic samples. We demonstrate the selectivity of our probe for the well-established human folate-binding protein dihydrofolate reductase and show no promiscuous labeling occurs with human caspase-3 or bovine serum albumin, which served as negative controls. Affinity-based enrichment of folate-binding proteins from an E. coli lysate in combination with mass spectrometry proteomics verified the ability of our probe to isolate low-abundance folate-dependent proteins. We envision that our probe will serve as a tool to elucidate the roles of commensal microbial folate-binding proteins in health and microbiome-related diseases.
Collapse
Affiliation(s)
- Akihiro Takamura
- Departments of Molecular Medicine and Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA; Biological Science Research, Kao Corporation, 2606 Akabane, Ichikai-machi, Haga-gun, Tochigi 3213497, Japan
| | - Peter S Thuy-Boun
- Departments of Molecular Medicine and Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Seiya Kitamura
- Departments of Molecular Medicine and Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Zhen Han
- Departments of Molecular Medicine and Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Dennis W Wolan
- Departments of Molecular Medicine and Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
| |
Collapse
|
20
|
Huang W, Kane MA. MAPLE: A Microbiome Analysis Pipeline Enabling Optimal Peptide Search and Comparative Taxonomic and Functional Analysis. J Proteome Res 2021; 20:2882-2894. [PMID: 33848166 DOI: 10.1021/acs.jproteome.1c00114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Metaproteomics by mass spectrometry (MS) is a powerful approach to profile a large number of proteins expressed by all organisms in a highly complex biological or ecological sample, which is able to provide a direct and quantitative assessment of the functional makeup of a microbiota. The human gastrointestinal microbiota has been found playing important roles in human physiology and health, and metaproteomics has been shown to shed light on multiple novel associations between microbiota and diseases. MS-powered proteomics generally relies on genome data to define search space. However, metaproteomics, which simultaneously analyzes all proteins from hundreds to thousands of species, faces significant challenges regarding database search and interpretation of results. To overcome these obstacles, we have developed a user-friendly microbiome analysis pipeline (MAPLE, freely downloadable at http://maple.rx.umaryland.edu/), which is able to define an optimal search space by inferring proteomes specific to samples following the principle of parsimony. MAPLE facilitates highly comparable or better peptide identification compared to a sample-specific metagenome-guided search. In addition, we implemented an automated peptide-centric enrichment analysis function in MAPLE to address issues of traditional protein-centric comparison, enabling straightforward and comprehensive comparison of taxonomic and functional makeup between microbiota.
Collapse
Affiliation(s)
- Weiliang Huang
- Department of Pharmaceutical Sciences, University of Maryland, School of Pharmacy, Baltimore, Maryland 21201, United States
| | - Maureen A Kane
- Department of Pharmaceutical Sciences, University of Maryland, School of Pharmacy, Baltimore, Maryland 21201, United States
| |
Collapse
|
21
|
Li L, Figeys D. Proteomics and Metaproteomics Add Functional, Taxonomic and Biomass Dimensions to Modeling the Ecosystem at the Mucosal-luminal Interface. Mol Cell Proteomics 2020; 19:1409-1417. [PMID: 32581040 PMCID: PMC8143649 DOI: 10.1074/mcp.r120.002051] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 06/04/2020] [Indexed: 12/19/2022] Open
Abstract
Recent efforts in gut microbiome studies have highlighted the importance of explicitly describing the ecological processes beyond correlative analysis. However, we are still at the early stage of understanding the organizational principles of the gut ecosystem, partially because of the limited information provided by currently used analytical tools in ecological modeling practices. Proteomics and metaproteomics can provide a number of insights for ecological studies, including biomass, matter and energy flow, and functional diversity. In this Mini Review, we discuss proteomics and metaproteomics-based experimental strategies that can contribute to studying the ecology, in particular at the mucosal-luminal interface (MLI) where the direct host-microbiome interaction happens. These strategies include isolation protocols for different MLI components, enrichment methods to obtain designated array of proteins, probing for specific pathways, and isotopic labeling for tracking nutrient flow. Integration of these technologies can generate spatiotemporal and site-specific biological information that supports mathematical modeling of the ecosystem at the MLI.
Collapse
Affiliation(s)
- Leyuan Li
- Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
| | - Daniel Figeys
- Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology, Faculty of Medicine, University of Ottawa, Ottawa, Canada.
| |
Collapse
|
22
|
Couvillion SP, Agrawal N, Colby SM, Brandvold KR, Metz TO. Who Is Metabolizing What? Discovering Novel Biomolecules in the Microbiome and the Organisms Who Make Them. Front Cell Infect Microbiol 2020; 10:388. [PMID: 32850487 PMCID: PMC7410922 DOI: 10.3389/fcimb.2020.00388] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 06/25/2020] [Indexed: 12/14/2022] Open
Abstract
Even as the field of microbiome research has made huge strides in mapping microbial community composition in a variety of environments and organisms, explaining the phenotypic influences on the host by microbial taxa-both known and unknown-and their specific functions still remain major challenges. A pressing need is the ability to assign specific functions in terms of enzymes and small molecules to specific taxa or groups of taxa in the community. This knowledge will be crucial for advancing personalized therapies based on the targeted modulation of microbes or metabolites that have predictable outcomes to benefit the human host. This perspective article advocates for the combined use of standards-free metabolomics and activity-based protein profiling strategies to address this gap in functional knowledge in microbiome research via the identification of novel biomolecules and the attribution of their production to specific microbial taxa.
Collapse
Affiliation(s)
- Sneha P. Couvillion
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Neha Agrawal
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Sean M. Colby
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Kristoffer R. Brandvold
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
- Elson S. Floyd College of Medicine, Washington State University, Spokane, WA, United States
| | - Thomas O. Metz
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| |
Collapse
|
23
|
Wang Y, Zhou Y, Xiao X, Zheng J, Zhou H. Metaproteomics: A strategy to study the taxonomy and functionality of the gut microbiota. J Proteomics 2020; 219:103737. [DOI: 10.1016/j.jprot.2020.103737] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 03/07/2020] [Accepted: 03/10/2020] [Indexed: 12/15/2022]
|
24
|
Kriaa A, Jablaoui A, Mkaouar H, Akermi N, Maguin E, Rhimi M. Serine proteases at the cutting edge of IBD: Focus on gastrointestinal inflammation. FASEB J 2020; 34:7270-7282. [PMID: 32307770 DOI: 10.1096/fj.202000031rr] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 03/27/2020] [Accepted: 03/28/2020] [Indexed: 12/15/2022]
Abstract
Serine proteases have been long recognized to coordinate many physiological processes and play key roles in regulating the inflammatory response. Accordingly, their dysregulation has been regularly associated with several inflammatory disorders and suggested as a central mechanism in the pathophysiology of digestive inflammation. So far, studies addressing the proteolytic homeostasis in the gut have mainly focused on host serine proteases as candidates of interest, while largely ignoring the potential contribution of their bacterial counterparts. The human gut microbiota comprises a complex ecosystem that contributes to host health and disease. Yet, our understanding of microbially produced serine proteases and investigation of whether they are causally linked to IBD is still in its infancy. In this review, we highlight recent advances in the emerging roles of host and bacterial serine proteases in digestive inflammation. We also discuss the application of available tools in the gut to monitor disease-related serine proteases. An exhaustive representation and understanding of such functional potential would help in closing existing gaps in mechanistic knowledge.
Collapse
Affiliation(s)
- Aicha Kriaa
- Microbiota Interaction with Human and Animal Team (MIHA), Micalis Institute, AgroParisTech, Université Paris-Saclay, INRAE, Jouy-en-Josas, France
| | - Amin Jablaoui
- Microbiota Interaction with Human and Animal Team (MIHA), Micalis Institute, AgroParisTech, Université Paris-Saclay, INRAE, Jouy-en-Josas, France
| | - Héla Mkaouar
- Microbiota Interaction with Human and Animal Team (MIHA), Micalis Institute, AgroParisTech, Université Paris-Saclay, INRAE, Jouy-en-Josas, France
| | - Nizar Akermi
- Microbiota Interaction with Human and Animal Team (MIHA), Micalis Institute, AgroParisTech, Université Paris-Saclay, INRAE, Jouy-en-Josas, France
| | - Emmanuelle Maguin
- Microbiota Interaction with Human and Animal Team (MIHA), Micalis Institute, AgroParisTech, Université Paris-Saclay, INRAE, Jouy-en-Josas, France
| | - Moez Rhimi
- Microbiota Interaction with Human and Animal Team (MIHA), Micalis Institute, AgroParisTech, Université Paris-Saclay, INRAE, Jouy-en-Josas, France
| |
Collapse
|
25
|
Mainoli B, Hirota S, Edgington-mitchell LE, Lu C, Dufour A. Proteomics and Imaging in Crohn’s Disease: TAILS of Unlikely Allies. Trends Pharmacol Sci 2020; 41:74-84. [DOI: 10.1016/j.tips.2019.11.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 11/05/2019] [Accepted: 11/27/2019] [Indexed: 12/12/2022]
|
26
|
Jariwala PB, Pellock SJ, Goldfarb D, Cloer EW, Artola M, Simpson JB, Bhatt AP, Walton WG, Roberts LR, Major MB, Davies GJ, Overkleeft HS, Redinbo MR. Discovering the Microbial Enzymes Driving Drug Toxicity with Activity-Based Protein Profiling. ACS Chem Biol 2020; 15:217-225. [PMID: 31774274 PMCID: PMC7321802 DOI: 10.1021/acschembio.9b00788] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
It is increasingly clear that interindividual variability in human gut microbial composition contributes to differential drug responses. For example, gastrointestinal (GI) toxicity is not observed in all patients treated with the anticancer drug irinotecan, and it has been suggested that this variability is a result of differences in the types and levels of gut bacterial β-glucuronidases (GUSs). GUS enzymes promote drug toxicity by hydrolyzing the inactive drug-glucuronide conjugate back to the active drug, which damages the GI epithelium. Proteomics-based identification of the exact GUS enzymes responsible for drug reactivation from the complexity of the human microbiota has not been accomplished, however. Here, we discover the specific bacterial GUS enzymes that generate SN-38, the active and toxic metabolite of irinotecan, from human fecal samples using a unique activity-based protein profiling (ABPP) platform. We identify and quantify gut bacterial GUS enzymes from human feces with an ABPP-enabled proteomics pipeline and then integrate this information with ex vivo kinetics to pinpoint the specific GUS enzymes responsible for SN-38 reactivation. Furthermore, the same approach also reveals the molecular basis for differential gut bacterial GUS inhibition observed between human fecal samples. Taken together, this work provides an unprecedented technical and bioinformatics pipeline to discover the microbial enzymes responsible for specific reactions from the complexity of human feces. Identifying such microbial enzymes may lead to precision biomarkers and novel drug targets to advance the promise of personalized medicine.
Collapse
Affiliation(s)
- Parth B. Jariwala
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Samuel J. Pellock
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Dennis Goldfarb
- Institute for Informatics, Washington University, St. Louis, Missouri 63130, United States
- Department of Cell Biology and Physiology, Washington University, St. Louis, Missouri 63130, United States
| | - Erica W. Cloer
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Marta Artola
- Department of Bioorganic Synthesis, Leiden Institute of Chemistry, Leiden University, Leiden 2311, The Netherlands
| | - Joshua B. Simpson
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Aadra P. Bhatt
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - William G. Walton
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Lee R. Roberts
- Exploratory Science Center, Merck & Company Inc., Cambridge, Massachusetts 02141, United States
| | - Michael B. Major
- Department of Cell Biology and Physiology, Washington University, St. Louis, Missouri 63130, United States
- Department of Otolaryngology, Washington University, St. Louis, Missouri 63130, United States
| | - Gideon J. Davies
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, U.K
| | - Herman S. Overkleeft
- Department of Bioorganic Synthesis, Leiden Institute of Chemistry, Leiden University, Leiden 2311, The Netherlands
| | - Matthew R. Redinbo
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Integrated Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Departments of Biochemistry and Microbiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| |
Collapse
|
27
|
Keller LJ, Babin BM, Lakemeyer M, Bogyo M. Activity-based protein profiling in bacteria: Applications for identification of therapeutic targets and characterization of microbial communities. Curr Opin Chem Biol 2019; 54:45-53. [PMID: 31835131 DOI: 10.1016/j.cbpa.2019.10.007] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 10/09/2019] [Accepted: 10/23/2019] [Indexed: 02/07/2023]
Abstract
Activity-based protein profiling (ABPP) is a robust chemoproteomic technique that uses activity-based probes to globally measure endogenous enzymatic activity in complex proteomes. It has been utilized extensively to characterize human disease states and identify druggable targets in diverse disease conditions. ABPP has also recently found applications in microbiology. This includes using activity-based probes (ABPs) for functional studies of pathogenic bacteria as well as complex communities within a microbiome. This review will focus on recent advances in the use of ABPs to profile enzyme activity in disease models, screen for selective inhibitors of key enzymes, and develop imaging tools to better understand the host-bacterial interface.
Collapse
Affiliation(s)
- Laura J Keller
- Department of Chemical & Systems Biology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA, 94305, USA
| | - Brett M Babin
- Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA, 94305, USA
| | - Markus Lakemeyer
- Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA, 94305, USA
| | - Matthew Bogyo
- Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA, 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA, 94305, USA.
| |
Collapse
|
28
|
Zhang X, Li L, Butcher J, Stintzi A, Figeys D. Advancing functional and translational microbiome research using meta-omics approaches. Microbiome 2019; 7:154. [PMID: 31810497 PMCID: PMC6898977 DOI: 10.1186/s40168-019-0767-6] [Citation(s) in RCA: 127] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 11/11/2019] [Indexed: 05/05/2023]
Abstract
The gut microbiome has emerged as an important factor affecting human health and disease. The recent development of -omics approaches, including phylogenetic marker-based microbiome profiling, shotgun metagenomics, metatranscriptomics, metaproteomics, and metabolomics, has enabled efficient characterization of microbial communities. These techniques can provide strain-level taxonomic resolution of the taxa present in microbiomes, assess the potential functions encoded by the microbial community and quantify the metabolic activities occurring within a complex microbiome. The application of these meta-omics approaches to clinical samples has identified microbial species, metabolic pathways, and metabolites that are associated with the development and treatment of human diseases. These findings have further facilitated microbiome-targeted drug discovery and efforts to improve human health management. Recent in vitro and in vivo investigations have uncovered the presence of extensive drug-microbiome interactions. These interactions have also been shown to be important contributors to the disparate patient responses to treatment that are often observed during disease therapy. Therefore, developing techniques or frameworks that enable rapid screening, detailed evaluation, and accurate prediction of drug/host-microbiome interactions is critically important in the modern era of microbiome research and precision medicine. Here we review the current status of meta-omics techniques, including integrative multi-omics approaches, for characterizing the microbiome's functionality in the context of health and disease. We also summarize and discuss new frameworks for applying meta-omics approaches and microbiome assays to study drug-microbiome interactions. Lastly, we discuss and exemplify strategies for implementing microbiome-based precision medicines using these meta-omics approaches and high throughput microbiome assays.
Collapse
Affiliation(s)
- Xu Zhang
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario Canada
| | - Leyuan Li
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario Canada
| | - James Butcher
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario Canada
| | - Alain Stintzi
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario Canada
| | - Daniel Figeys
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario Canada
| |
Collapse
|
29
|
Abstract
The market of probiotics is growing dynamically for the food and supplements, which provides better health to an individual. Probiotics are used as dietary management for diseases, but it varies between regions and persons. Systems biology can help in resolving the strain specificity of probiotics by studying their genome level organization. In this review, we have compiled facets of systems biology and next-generation omics methods such as metagenomics, proteomics and metabolomics. These tools are crucial for the optimization of the metabolic processes in probiotics and hence, their use for human health. The limitations and challenges associated with the development of probiotics involve their stability and function in different individuals. Systems biology facilitates emerging metabolic engineering approaches to improve probiotics strain for their broader application. This review provides comprehensive and updated knowledge of engineered probiotics as therapeutics and various challenges in the development of engineered probiotics.
Collapse
Affiliation(s)
- Monika Yadav
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana 124001 India
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana 124001 India
| |
Collapse
|
30
|
Gordon MH, Anowai A, Young D, Das N, Campden RI, Sekhon H, Myers Z, Mainoli B, Chopra S, Thuy-Boun PS, Kizhakkedathu J, Bindra G, Jijon HB, Heitman S, Yates R, Wolan DW, Edgington-Mitchell LE, MacNaughton WK, Dufour A. N-Terminomics/TAILS Profiling of Proteases and Their Substrates in Ulcerative Colitis. ACS Chem Biol 2019; 14:2471-2483. [PMID: 31393699 DOI: 10.1021/acschembio.9b00608] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Dysregulated protease activity is often implicated in the initiation of inflammation and immune cell recruitment in gastrointestinal inflammatory diseases. Using N-terminomics/TAILS (terminal amine isotopic labeling of substrates), we compared proteases, along with their substrates and inhibitors, between colonic mucosal biopsies of healthy patients and those with ulcerative colitis (UC). Among the 1642 N-termini enriched using TAILS, increased endogenous processing of proteins was identified in UC compared to healthy patients. Changes in the reactome pathways for proteins associated with metabolism, adherens junction proteins (E-cadherin, liver-intestinal cadherin, catenin alpha-1, and catenin delta-1), and neutrophil degranulation were identified between the two groups. Increased neutrophil infiltration and distinct proteases observed in ulcerative colitis may result in extensive break down, altered processing, or increased remodeling of adherens junctions and other cellular functions. Analysis of the preferred proteolytic cleavage sites indicated that the majority of proteolytic activity and processing comes from host proteases, but that key microbial proteases may also play a role in maintaining homeostasis. Thus, the identification of distinct proteases and processing of their substrates improves the understanding of dysregulated proteolysis in normal intestinal physiology and ulcerative colitis.
Collapse
Affiliation(s)
- Marilyn H. Gordon
- Department of Physiology and Pharmacology, University of Calgary, Calgary, Alberta, Canada T2N 4N1
| | - Anthonia Anowai
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada T2N 4N1
- McCaig Institute for Bone and Joint Health, University of Calgary, Calgary, Alberta, Canada T2N 4N1
| | - Daniel Young
- Department of Physiology and Pharmacology, University of Calgary, Calgary, Alberta, Canada T2N 4N1
- McCaig Institute for Bone and Joint Health, University of Calgary, Calgary, Alberta, Canada T2N 4N1
| | - Nabangshu Das
- Department of Physiology and Pharmacology, University of Calgary, Calgary, Alberta, Canada T2N 4N1
- McCaig Institute for Bone and Joint Health, University of Calgary, Calgary, Alberta, Canada T2N 4N1
| | - Rhiannon I. Campden
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada T2N 4N1
- Department of Comparative Biology and Experimental Medicine, University of Calgary, Calgary, Alberta, Canada T2N 4N1
| | - Henna Sekhon
- Department of Physiology and Pharmacology, University of Calgary, Calgary, Alberta, Canada T2N 4N1
- McCaig Institute for Bone and Joint Health, University of Calgary, Calgary, Alberta, Canada T2N 4N1
| | - Zoe Myers
- Department of Physiology and Pharmacology, University of Calgary, Calgary, Alberta, Canada T2N 4N1
- McCaig Institute for Bone and Joint Health, University of Calgary, Calgary, Alberta, Canada T2N 4N1
| | - Barbara Mainoli
- Department of Physiology and Pharmacology, University of Calgary, Calgary, Alberta, Canada T2N 4N1
- McCaig Institute for Bone and Joint Health, University of Calgary, Calgary, Alberta, Canada T2N 4N1
| | - Sameeksha Chopra
- Department of Physiology and Pharmacology, University of Calgary, Calgary, Alberta, Canada T2N 4N1
- McCaig Institute for Bone and Joint Health, University of Calgary, Calgary, Alberta, Canada T2N 4N1
| | - Peter S. Thuy-Boun
- Departments of Molecular Medicine and Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Jayachandran Kizhakkedathu
- Department of Pathology and Laboratory Medicine and Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z2, Canada
| | - Gurmeet Bindra
- Department of Medicine, Division of Gastroenterology, University of Calgary, Calgary, Alberta, Canada T2N 4N1
| | - Humberto B. Jijon
- Department of Medicine, Division of Gastroenterology, University of Calgary, Calgary, Alberta, Canada T2N 4N1
| | - Steven Heitman
- Department of Medicine, Division of Gastroenterology, University of Calgary, Calgary, Alberta, Canada T2N 4N1
| | - Robin Yates
- Department of Comparative Biology and Experimental Medicine, University of Calgary, Calgary, Alberta, Canada T2N 4N1
| | - Dennis W. Wolan
- Departments of Molecular Medicine and Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Laura E. Edgington-Mitchell
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Victoria, Parkville, Australia
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
- Department of Oral and Maxillofacial Surgery, New York University College of Dentistry, Bluestone Center for Clinical Research, New York, New York, United States
| | - Wallace K. MacNaughton
- Department of Physiology and Pharmacology, University of Calgary, Calgary, Alberta, Canada T2N 4N1
| | - Antoine Dufour
- Department of Physiology and Pharmacology, University of Calgary, Calgary, Alberta, Canada T2N 4N1
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada T2N 4N1
- McCaig Institute for Bone and Joint Health, University of Calgary, Calgary, Alberta, Canada T2N 4N1
| |
Collapse
|
31
|
Thuy-Boun PS, Wolan DW. A glycal-based photoaffinity probe that enriches sialic acid binding proteins. Bioorg Med Chem Lett 2019; 29:2609-2612. [PMID: 31387789 DOI: 10.1016/j.bmcl.2019.07.054] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 07/29/2019] [Accepted: 07/31/2019] [Indexed: 12/22/2022]
Abstract
To identify sialic acid binding proteins from complex proteomes, three photocrosslinking affinity-based probes were constructed using Neu5Ac (5 and 6) and Neu5Ac2en (7) scaffolds. Kinetic inhibition assays and Western blotting revealed the Neu5Ac2en-based 7 to be an effective probe for the labeling of a purified gut microbial sialidase (BDI_2946) and a purified human sialic acid binding protein (hCD33). Additionally, LC-MS/MS affinity-based protein profiling verified the ability of 7 to enrich a low-abundance sialic acid binding protein (complement factor H) from human serum thus validating the utility of this probe in a complex context.
Collapse
Affiliation(s)
- Peter S Thuy-Boun
- Departments of Molecular Medicine and Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Dennis W Wolan
- Departments of Molecular Medicine and Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
| |
Collapse
|
32
|
Li L, Abou-Samra E, Ning Z, Zhang X, Mayne J, Wang J, Cheng K, Walker K, Stintzi A, Figeys D. An in vitro model maintaining taxon-specific functional activities of the gut microbiome. Nat Commun 2019; 10:4146. [PMID: 31515476 PMCID: PMC6742639 DOI: 10.1038/s41467-019-12087-8] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Accepted: 08/15/2019] [Indexed: 12/22/2022] Open
Abstract
In vitro gut microbiome models could provide timely and cost-efficient solutions to study microbiome responses to drugs. For this purpose, in vitro models that maintain the functional and compositional profiles of in vivo gut microbiomes would be extremely valuable. Here, we present a 96-deep well plate-based culturing model (MiPro) that maintains the functional and compositional profiles of individual gut microbiomes, as assessed by metaproteomics, while allowing a four-fold increase in viable bacteria counts. Comparison of taxon-specific functions between pre- and post-culture microbiomes shows a Pearson's correlation coefficient r of 0.83 ± 0.03. In addition, we show a high degree of correlation between gut microbiome responses to metformin in the MiPro model and those in mice fed a high-fat diet. We propose MiPro as an in vitro gut microbiome model for scalable investigation of drug-microbiome interactions such as during high-throughput drug screening.
Collapse
Affiliation(s)
- Leyuan Li
- Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
| | - Elias Abou-Samra
- Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
| | - Zhibin Ning
- Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
| | - Xu Zhang
- Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
| | - Janice Mayne
- Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
| | - Janet Wang
- Department of Statistical Sciences, Faculty of Arts and Science, University of Toronto, Toronto, Canada
| | - Kai Cheng
- Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
| | - Krystal Walker
- Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
| | - Alain Stintzi
- Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
| | - Daniel Figeys
- Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology, Faculty of Medicine, University of Ottawa, Ottawa, Canada.
- Canadian Institute for Advanced Research, Toronto, Canada.
| |
Collapse
|
33
|
Issa Isaac N, Philippe D, Nicholas A, Raoult D, Eric C. Metaproteomics of the human gut microbiota: Challenges and contributions to other OMICS. Clinical Mass Spectrometry 2019; 14 Pt A:18-30. [DOI: 10.1016/j.clinms.2019.06.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 06/02/2019] [Accepted: 06/03/2019] [Indexed: 12/22/2022]
|
34
|
Parasar B, Zhou H, Xiao X, Shi Q, Brito IL, Chang PV. Chemoproteomic Profiling of Gut Microbiota-Associated Bile Salt Hydrolase Activity. ACS Cent Sci 2019; 5:867-873. [PMID: 31139722 PMCID: PMC6535767 DOI: 10.1021/acscentsci.9b00147] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Indexed: 05/26/2023]
Abstract
The metagenome of the gut microbiome encodes tremendous potential for biosynthesizing and transforming small-molecule metabolites through the activities of enzymes expressed by intestinal bacteria. Accordingly, elucidating this metabolic network is critical for understanding how the gut microbiota contributes to health and disease. Bile acids, which are first biosynthesized in the liver, are modified in the gut by enzymes expressed by commensal bacteria into secondary bile acids, which regulate myriad host processes, including lipid metabolism, glucose metabolism, and immune homeostasis. The gateway reaction of secondary bile acid biosynthesis is mediated by bile salt hydrolases (BSHs), bacterial cysteine hydrolases whose action precedes other bile acid modifications within the gut. To assess how changes in bile acid metabolism mediated by certain intestinal microbiota impact gut physiology and pathobiology, methods are needed to directly examine the activities of BSHs because they are master regulators of intestinal bile acid metabolism. Here, we developed chemoproteomic tools to profile changes in gut microbiome-associated BSH activity. We showed that these probes can label active BSHs in model microorganisms, including relevant gut anaerobes, and in mouse gut microbiomes. Using these tools, we identified altered BSH activities in a murine model of inflammatory bowel disease, in this case, colitis induced by dextran sodium sulfate, leading to changes in bile acid metabolism that could impact host metabolism and immunity. Importantly, our findings reveal that alterations in BSH enzymatic activities within the gut microbiome do not correlate with changes in gene abundance as determined by metagenomic sequencing, highlighting the utility of chemoproteomic approaches for interrogating the metabolic activities of the gut microbiota.
Collapse
Affiliation(s)
- Bibudha Parasar
- Department
of Chemistry and Chemical Biology, Department of Microbiology, Meinig School of Biomedical
Engineering, Center for Infection and Pathobiology, Cornell Institute of Host-Microbe
Interactions & Disease, and Department of Microbiology and Immunology, Cornell University, Ithaca, New York 14853, United States
| | - Hao Zhou
- Department
of Chemistry and Chemical Biology, Department of Microbiology, Meinig School of Biomedical
Engineering, Center for Infection and Pathobiology, Cornell Institute of Host-Microbe
Interactions & Disease, and Department of Microbiology and Immunology, Cornell University, Ithaca, New York 14853, United States
| | - Xieyue Xiao
- Department
of Chemistry and Chemical Biology, Department of Microbiology, Meinig School of Biomedical
Engineering, Center for Infection and Pathobiology, Cornell Institute of Host-Microbe
Interactions & Disease, and Department of Microbiology and Immunology, Cornell University, Ithaca, New York 14853, United States
| | - Qiaojuan Shi
- Department
of Chemistry and Chemical Biology, Department of Microbiology, Meinig School of Biomedical
Engineering, Center for Infection and Pathobiology, Cornell Institute of Host-Microbe
Interactions & Disease, and Department of Microbiology and Immunology, Cornell University, Ithaca, New York 14853, United States
| | - Ilana L. Brito
- Department
of Chemistry and Chemical Biology, Department of Microbiology, Meinig School of Biomedical
Engineering, Center for Infection and Pathobiology, Cornell Institute of Host-Microbe
Interactions & Disease, and Department of Microbiology and Immunology, Cornell University, Ithaca, New York 14853, United States
| | - Pamela V. Chang
- Department
of Chemistry and Chemical Biology, Department of Microbiology, Meinig School of Biomedical
Engineering, Center for Infection and Pathobiology, Cornell Institute of Host-Microbe
Interactions & Disease, and Department of Microbiology and Immunology, Cornell University, Ithaca, New York 14853, United States
| |
Collapse
|
35
|
Abstract
Metaproteomics is the large-scale identification and quantification of proteins from microbial communities and thus provides direct insight into the phenotypes of microorganisms on the molecular level. Initially, metaproteomics was mainly used to assess the "expressed" metabolism and physiology of microbial community members. However, recently developed metaproteomic tools allow quantification of per-species biomass to determine community structure, in situ carbon sources of community members, and the uptake of labeled substrates by community members. In this perspective, I provide a brief overview of the questions that we can currently address, as well as new metaproteomics-based approaches that we and others are developing to address even more questions in the study of microbial communities and plant and animal microbiota. I also highlight some areas and technologies where I anticipate developments and potentially major breakthroughs in the next 5 years and beyond.
Collapse
|
36
|
Levi Mortera S, Soggiu A, Vernocchi P, Del Chierico F, Piras C, Carsetti R, Marzano V, Britti D, Urbani A, Roncada P, Putignani L. Metaproteomic investigation to assess gut microbiota shaping in newborn mice: A combined taxonomic, functional and quantitative approach. J Proteomics 2019; 203:103378. [PMID: 31102759 DOI: 10.1016/j.jprot.2019.103378] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 04/23/2019] [Accepted: 05/13/2019] [Indexed: 12/16/2022]
Abstract
Breastfeeding is nowadays known to be one of the most critical factors contributing to the development of an efficient immune system. In the last decade, a consistent number of pieces of evidence demonstrated the relationship between a healthy organism and its gut microbiota. However, this link is still not fully understood and requires further investigation. We recently adopted a murine model to describe the impact of either maternal milk or parental genetic background, on the composition of the gut microbial population in the first weeks of life. A metaproteomic approach to such complex environments is a big challenge that requires a strong effort in both data production and analysis, including the set-up of dedicated multitasking bioinformatics pipelines. Herein we present an LC-MS/MS based investigation to monitor mouse gut microbiota in the early life, aiming at characterizing its functions and metabolic activities together with a taxonomic description in terms of operational taxonomic units. We provided a quantitative evaluation of bacterial metaproteins, taking into account differential expression results in relation to the functional and taxonomic classification, particularly with proteins from orthologues groups. This allowed the reduction of the bias arising from the presence of a high number of shared peptides, and proteins, among different bacterial species. We also focused on host mucosal proteome and its modulation, according to different microbiota composition. SIGNIFICANCE: This paper would represent a reference work for investigations on gut microbiota in early life, from both a microbiological and a functional proteomic point of view. We focused on the shaping of the mouse gut microbiota in dependence on the feeding modality, defining a reliable taxonomic description, highlighting some functional characteristics of the microbial community, and performing a first quantitative evaluation by data independent analysis in metaproteomics.
Collapse
Affiliation(s)
| | - Alessio Soggiu
- Department of Veterinary Medicine, University of Milan, Milan, Italy
| | - Pamela Vernocchi
- Human Microbiome Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | | | - Cristian Piras
- Department of Veterinary Medicine, University of Milan, Milan, Italy
| | - Rita Carsetti
- B cell Pathophysiology Unit, Immunology Research Area and Unit of Diagnostic Immunology, Department of Laboratories, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Valeria Marzano
- Human Microbiome Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Domenico Britti
- C.I.S. - Interdepartmental Services Centre of Veterinary for Human and Animal Health, University of Catanzaro "Magna Græcia", Catanzaro, Italy.; Department of Health Sciences, University of Catanzaro "Magna Græcia", Catanzaro, Italy
| | - Andrea Urbani
- Catholic University of Sacred Heart, Rome, Italy; Fondazione Policlinico Universitario A. Gemelli, IRCCS, Rome, Italy
| | - Paola Roncada
- Department of Health Sciences, University of Catanzaro "Magna Græcia", Catanzaro, Italy
| | - Lorenza Putignani
- Parasitology Unit and Human Microbiome Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy.
| |
Collapse
|
37
|
Abstract
The microbiome is emerging as a prominent factor affecting human health, and its dysbiosis is associated with various diseases. Compositional profiling of microbiome is increasingly being supplemented with functional characterization. Metaproteomics is intrinsically focused on functional changes and therefore will be an important tool in those studies of the human microbiome. In the past decade, development of new experimental and bioinformatic approaches for metaproteomics has enabled large-scale human metaproteomic studies. However, challenges still exist, and there remains a lack of standardizations and guidelines for properly performing metaproteomic studies on human microbiome. Herein, we provide a perspective of recent developments, the challenges faced, and the future directions of metaproteomics and its applications. In addition, we propose a set of guidelines/recommendations for performing and reporting the results from metaproteomic experiments for the study of human microbiomes. We anticipate that these guidelines will be optimized further as more metaproteomic questions are raised and addressed, and metaproteomic applications are published, so that they are eventually recognized and applied in the field.
Collapse
Affiliation(s)
- Xu Zhang
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine , University of Ottawa , Ottawa , Ontario K1H 8M5 , Canada
| | - Daniel Figeys
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine , University of Ottawa , Ottawa , Ontario K1H 8M5 , Canada
| |
Collapse
|
38
|
Abstract
Covering: up to the end of 2017 The human body is composed of an equal number of human and microbial cells. While the microbial community inhabiting the human gastrointestinal tract plays an essential role in host health, these organisms have also been connected to various diseases. Yet, the gut microbial functions that modulate host biology are not well established. In this review, we describe metabolic functions of the human gut microbiota that involve metalloenzymes. These activities enable gut microbial colonization, mediate interactions with the host, and impact human health and disease. We highlight cases in which enzyme characterization has advanced our understanding of the gut microbiota and examples that illustrate the diverse ways in which metalloenzymes facilitate both essential and unique functions of this community. Finally, we analyze Human Microbiome Project sequencing datasets to assess the distribution of a prominent family of metalloenzymes in human-associated microbial communities, guiding future enzyme characterization efforts.
Collapse
|
39
|
Abstract
We designed a metaproteomic analysis method (ComPIL) to accommodate the ever-increasing number of sequences against which experimental shotgun proteomics spectra could be accurately and rapidly queried. Our objective was to create these large databases for the analysis of complex metasamples with unknown composition, including those derived from human, animal, and environmental microbiomes. The amount of high-throughput sequencing data has substantially increased since our original database was assembled in 2014. Here, we present a rebuild of the ComPIL libraries comprised of updated publicly disseminated sequence data as well as a modified version of the search engine ProLuCID-ComPIL optimized for querying experimental spectra. ComPIL 2.0 consists of 113 million protein records and roughly 4.8 billion unique tryptic peptide sequences and is 2.3 times the size of our original version. We searched a data set collected on a healthy human gut microbiome proteomic sample and compared the results to demonstrate that ComPIL 2.0 showed a substantial increase in the number of unique identified peptides and proteins compared to the first ComPIL version. The high confidence of protein identification and accuracy demonstrated by the use of ComPIL 2.0 may encourage the method's application for large-scale proteomic annotation of complex protein systems.
Collapse
Affiliation(s)
- Sung Kyu (Robin) Park
- Department of Molecular Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
- Department of Neuroscience, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Titus Jung
- Department of Molecular Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
- Department of Neuroscience, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Peter S. Thuy-Boun
- Department of Molecular Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Ana Y. Wang
- Department of Molecular Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - John R. Yates
- Department of Molecular Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
- Department of Neuroscience, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Dennis W. Wolan
- Department of Molecular Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| |
Collapse
|
40
|
Abstract
Background: Cervical-vaginal fluid (CVF) hydrates the mucosa of the lower female reproductive tract and is known to contain numerous proteases. The low pH of CVF (4.5 or below in healthy women of reproductive age) is a uniquely human attribute and poses a challenge for the proteolytic functioning of the proteases identified in this complex biological fluid. Despite the abundance of certain proteases in CVF, the proteolytic activity and function of proteases in CVF is not well characterized. Methods: In the present study, we employed fluorogenic substrate screening to investigate the influence of pH and inhibitory compounds on the proteolytic activity in CVF. Activity-based probe (ABP) proteomics has evolved as a powerful tool to investigate active proteases within complex proteomes and a trypsin-specific ABP was used to identify active proteases in CVF. Results: Serine proteases are among the most abundant proteins in the CVF proteome. Labeling human CVF samples with the trypsin-specific ABP revealed serine proteases transmembrane protein serine 11D and kallikrein-related peptidase 13 as active proteases in CVF. Furthermore, we demonstrated that the proteolytic activity in CVF is highly pH-dependent with an almost absolute inhibition of trypsin-like proteolytic activity at physiological pH levels. Conclusions: These findings provide a framework to understand proteolytic activity in CVF. Furthermore, the present results provide clues for a novel regulatory mechanism in which fluctuations in CVF pH have the potential to control the catalytic activity in the lower female reproductive tract.
Collapse
Affiliation(s)
- Carla M J Muytjens
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada.,Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Toronto, Canada
| | - Yijing Yu
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada.,Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Toronto, Canada
| | - Eleftherios P Diamandis
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada.,Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Toronto, Canada.,Department of Clinical Biochemistry, University Health Network, Canada, Toronto, Canada
| |
Collapse
|
41
|
Kunath BJ, Minniti G, Skaugen M, Hagen LH, Vaaje-Kolstad G, Eijsink VGH, Pope PB, Arntzen MØ. Metaproteomics: Sample Preparation and Methodological Considerations. Advances in Experimental Medicine and Biology 2019; 1073:187-215. [DOI: 10.1007/978-3-030-12298-0_8] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
42
|
Abstract
The lysis and extraction of soluble bacterial proteins from cells is a common practice for proteomics analyses, but insoluble bacterial biomasses are often left behind. Here, we show that with triflic acid treatment, the insoluble bacterial biomass of Gram- and Gram+ bacteria can be rendered soluble. We use LC-MS/MS shotgun proteomics to show that bacterial proteins in the soluble and insoluble postlysis fractions differ significantly. Additionally, in the case of Gram- Pseudomonas aeruginosa, triflic acid treatment enables the enrichment of cell-envelope-associated proteins. Finally, we apply triflic acid to a human microbiome sample to show that this treatment is robust and enables the identification of a new, complementary subset of proteins from a complex microbial mixture.
Collapse
Affiliation(s)
- Ana Y Wang
- Department of Molecular Medicine and Department of Integrative Structural and Computational Biology , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States
| | - Peter S Thuy-Boun
- Department of Molecular Medicine and Department of Integrative Structural and Computational Biology , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States
| | - Gregory S Stupp
- Department of Molecular Medicine and Department of Integrative Structural and Computational Biology , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States
| | - Andrew I Su
- Department of Molecular Medicine and Department of Integrative Structural and Computational Biology , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States
| | - Dennis W Wolan
- Department of Molecular Medicine and Department of Integrative Structural and Computational Biology , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States
| |
Collapse
|
43
|
Heintz-Buschart A, Wilmes P. Human Gut Microbiome: Function Matters. Trends Microbiol 2018; 26:563-574. [DOI: 10.1016/j.tim.2017.11.002] [Citation(s) in RCA: 296] [Impact Index Per Article: 49.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 10/29/2017] [Accepted: 11/03/2017] [Indexed: 12/16/2022]
|
44
|
Affiliation(s)
- Megan H. Wright
- Astbury Centre for Structural Molecular Biology; School of Chemistry; University of Leeds; Leeds LS2 9JT United Kingdom
| |
Collapse
|
45
|
Yurkovich JT, Palsson BO. Quantitative -omic data empowers bottom-up systems biology. Curr Opin Biotechnol 2018; 51:130-136. [DOI: 10.1016/j.copbio.2018.01.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 01/09/2018] [Accepted: 01/09/2018] [Indexed: 12/24/2022]
|
46
|
Schatschneider S, Abdelrazig S, Safo L, Henstra AM, Millat T, Kim DH, Winzer K, Minton NP, Barrett DA. Quantitative Isotope-Dilution High-Resolution-Mass-Spectrometry Analysis of Multiple Intracellular Metabolites in Clostridium autoethanogenum with Uniformly 13C-Labeled Standards Derived from Spirulina. Anal Chem 2018. [PMID: 29533656 DOI: 10.1021/acs.analchem.7b04758] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
We have investigated the applicability of commercially available lyophilized spirulina ( Arthrospira platensis), a microorganism uniformly labeled with 13C, as a readily accessible source of multiple 13C-labeled metabolites suitable as internal standards for the quantitative determination of intracellular bacterial metabolites. Metabolites of interest were analyzed by hydrophilic-interaction liquid chromatography coupled with high-resolution mass spectrometry. Multiple internal standards obtained from uniformly (U)-13C-labeled extracts from spirulina were used to enable isotope-dilution mass spectrometry (IDMS) in the identification and quantification of intracellular metabolites. Extraction of the intracellular metabolites of Clostridium autoethanogenum using 2:1:1 chloroform/methanol/water was found to be the optimal method in comparison with freeze-thaw, homogenization, and sonication methods. The limits of quantification were ≤1 μM with excellent linearity for all of the calibration curves ( R2 ≥ 0.99) for 74 metabolites. The precision and accuracy were found to be within relative standard deviations (RSDs) of 15% for 49 of the metabolites and within RSDs of 20% for all of the metabolites. The method was applied to study the effects of feeding different levels of carbon monoxide (as a carbon source) on the central metabolism and Wood-Ljungdahl pathway of C. autoethanogenum grown in continuous culture over 35 days. Using LC-IDMS with U-13C spirulina allowed the successful quantification of 52 metabolites in the samples, including amino acids, carboxylic acids, sugar phosphates, purines, and pyrimidines. The method provided absolute quantitative data on intracellular metabolites that was suitable for computational modeling to understand and optimize the C. autoethanogenum metabolic pathways active in gas fermentation.
Collapse
Affiliation(s)
- Sarah Schatschneider
- Centre for Analytical Bioscience, School of Pharmacy , University of Nottingham , Nottingham NG7 2RD , U.K
| | - Salah Abdelrazig
- Centre for Analytical Bioscience, School of Pharmacy , University of Nottingham , Nottingham NG7 2RD , U.K
| | - Laudina Safo
- Centre for Analytical Bioscience, School of Pharmacy , University of Nottingham , Nottingham NG7 2RD , U.K
| | - Anne M Henstra
- Clostridia Research Group, SBRC-Nottingham, a BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences , University of Nottingham , Nottingham NG7 2RD , U.K
| | - Thomas Millat
- Clostridia Research Group, SBRC-Nottingham, a BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences , University of Nottingham , Nottingham NG7 2RD , U.K
| | - Dong-Hyun Kim
- Centre for Analytical Bioscience, School of Pharmacy , University of Nottingham , Nottingham NG7 2RD , U.K
| | - Klaus Winzer
- Clostridia Research Group, SBRC-Nottingham, a BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences , University of Nottingham , Nottingham NG7 2RD , U.K
| | - Nigel P Minton
- Clostridia Research Group, SBRC-Nottingham, a BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences , University of Nottingham , Nottingham NG7 2RD , U.K
| | - David A Barrett
- Centre for Analytical Bioscience, School of Pharmacy , University of Nottingham , Nottingham NG7 2RD , U.K
| |
Collapse
|
47
|
Xiao J, Tanca A, Jia B, Yang R, Wang B, Zhang Y, Li J. Metagenomic Taxonomy-Guided Database-Searching Strategy for Improving Metaproteomic Analysis. J Proteome Res 2018; 17:1596-1605. [DOI: 10.1021/acs.jproteome.7b00894] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Jinqiu Xiao
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, People’s Republic of China
| | - Alessandro Tanca
- Porto Conte Ricerche, Science and Technology Park of Sardinia, Tramariglio, Alghero, Italy
| | - Ben Jia
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, People’s Republic of China
| | - Runqing Yang
- College of Computer Science and Technology, Zhejiang University, Hangzhou 310027, People’s Republic of China
| | - Bo Wang
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, People’s Republic of China
| | - Yu Zhang
- Institute of Oceanography, Shanghai Jiao Tong University, Shanghai 200240, People’s Republic of China
| | - Jing Li
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, People’s Republic of China
| |
Collapse
|
48
|
Moon C, Stupp GS, Su AI, Wolan DW. Metaproteomics of Colonic Microbiota Unveils Discrete Protein Functions among Colitic Mice and Control Groups. Proteomics 2018; 18:10.1002/pmic.201700391. [PMID: 29319931 PMCID: PMC5921860 DOI: 10.1002/pmic.201700391] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 12/19/2017] [Indexed: 12/14/2022]
Abstract
Metaproteomics can greatly assist established high-throughput sequencing methodologies to provide systems biological insights into the alterations of microbial protein functionalities correlated with disease-associated dysbiosis of the intestinal microbiota. Here, the authors utilize the well-characterized murine T cell transfer model of colitis to find specific changes within the intestinal luminal proteome associated with inflammation. MS proteomic analysis of colonic samples permitted the identification of ≈10 000-12 000 unique peptides that corresponded to 5610 protein clusters identified across three groups, including the colitic Rag1-/- T cell recipients, isogenic Rag1-/- controls, and wild-type mice. The authors demonstrate that the colitic mice exhibited a significant increase in Proteobacteria and Verrucomicrobia and show that such alterations in the microbial communities contributed to the enrichment of specific proteins with transcription and translation gene ontology terms. In combination with 16S sequencing, the authors' metaproteomics-based microbiome studies provide a foundation for assessing alterations in intestinal luminal protein functionalities in a robust and well-characterized mouse model of colitis, and set the stage for future studies to further explore the functional mechanisms of altered protein functionalities associated with dysbiosis and inflammation.
Collapse
Affiliation(s)
- Clara Moon
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Gregory S Stupp
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Andrew I Su
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Dennis W Wolan
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| |
Collapse
|
49
|
Whidbey C, Wright AT. Activity-Based Protein Profiling-Enabling Multimodal Functional Studies of Microbial Communities. Curr Top Microbiol Immunol 2019; 420:1-21. [PMID: 30406866 DOI: 10.1007/82_2018_128] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Microorganisms living in community are critical to life on Earth, playing numerous and profound roles in the environment and human and animal health. Though their essentiality to life is clear, the mechanistic underpinnings of community structure, interactions, and functions are largely unexplored and in need of function-dependent technologies to unravel the mysteries. Activity-based protein profiling offers unprecedented molecular-level characterization of functions within microbial communities and provides an avenue to determine how external exposures result in functional alterations to microbiomes. Herein, we illuminate the current state and prospective contributions of ABPP as it relates to microbial communities. We provide details on the design, development, and validation of probes, challenges associated with probing in complex microbial communities, provide some specific examples of the biological applications of ABPP in microbes and microbial communities, and highlight potential areas for development. The future of ABPP holds real promise for understanding and considerable impact in microbiome studies associated with personalized medicine, precision agriculture, veterinary health, environmental studies, and beyond.
Collapse
|
50
|
Abstract
Activity-based protein profiling (ABPP) is a technique for selectively detecting reactive amino acids in complex proteomes with the aid of chemical probes. Using probes that target catalytically active enzymes, ABPP can rapidly define the functional proteome of a biological system. In recent years, this approach has been increasingly applied to globally profile enzymes active at the host-pathogen interface of microbial infections. From in vitro co-culture systems to animal models of infection, these studies have revealed enzyme-mediated mechanisms of microbial pathogenicity, host immunity, and metabolic adaptation that dynamically shape pathogen interactions with the host.
Collapse
Affiliation(s)
- Yekaterina Kovalyova
- Microbial Sciences Institute, Yale University, West Haven, CT, 06516, USA.,Department of Chemistry, Yale University, New Haven, CT, 06511, USA
| | - Stavroula K Hatzios
- Microbial Sciences Institute, Yale University, West Haven, CT, 06516, USA. .,Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, 06511, USA. .,Department of Chemistry, Yale University, New Haven, CT, 06511, USA.
| |
Collapse
|