1
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Schweke H, Pacesa M, Levin T, Goverde CA, Kumar P, Duhoo Y, Dornfeld LJ, Dubreuil B, Georgeon S, Ovchinnikov S, Woolfson DN, Correia BE, Dey S, Levy ED. An atlas of protein homo-oligomerization across domains of life. Cell 2024; 187:999-1010.e15. [PMID: 38325366 DOI: 10.1016/j.cell.2024.01.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 11/03/2023] [Accepted: 01/15/2024] [Indexed: 02/09/2024]
Abstract
Protein structures are essential to understanding cellular processes in molecular detail. While advances in artificial intelligence revealed the tertiary structure of proteins at scale, their quaternary structure remains mostly unknown. We devise a scalable strategy based on AlphaFold2 to predict homo-oligomeric assemblies across four proteomes spanning the tree of life. Our results suggest that approximately 45% of an archaeal proteome and a bacterial proteome and 20% of two eukaryotic proteomes form homomers. Our predictions accurately capture protein homo-oligomerization, recapitulate megadalton complexes, and unveil hundreds of homo-oligomer types, including three confirmed experimentally by structure determination. Integrating these datasets with omics information suggests that a majority of known protein complexes are symmetric. Finally, these datasets provide a structural context for interpreting disease mutations and reveal coiled-coil regions as major enablers of quaternary structure evolution in human. Our strategy is applicable to any organism and provides a comprehensive view of homo-oligomerization in proteomes.
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Affiliation(s)
- Hugo Schweke
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Martin Pacesa
- Laboratory of Protein Design and Immunoengineering, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Tal Levin
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Casper A Goverde
- Laboratory of Protein Design and Immunoengineering, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Prasun Kumar
- School of Chemistry, University of Bristol, Bristol BS8 1TS, UK; School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK; Bristol BioDesign Institute, University of Bristol, Life Sciences Building, Bristol BS8 1TQ, UK; Max Planck-Bristol Centre for Minimal Biology, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
| | - Yoan Duhoo
- Protein Production and Structure Characterization Core Facility (PTPSP), School of Life Sciences, École polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Lars J Dornfeld
- Laboratory of Protein Design and Immunoengineering, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Benjamin Dubreuil
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Sandrine Georgeon
- Laboratory of Protein Design and Immunoengineering, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Sergey Ovchinnikov
- John Harvard Distinguished Science Fellowship Program, Harvard University, Cambridge, MA, USA
| | - Derek N Woolfson
- School of Chemistry, University of Bristol, Bristol BS8 1TS, UK; School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK; Bristol BioDesign Institute, University of Bristol, Life Sciences Building, Bristol BS8 1TQ, UK; Max Planck-Bristol Centre for Minimal Biology, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK.
| | - Bruno E Correia
- Laboratory of Protein Design and Immunoengineering, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland.
| | - Sucharita Dey
- Department of Bioscience and Bioengineering, Indian Institute of Technology Jodhpur, Rajasthan, India.
| | - Emmanuel D Levy
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel.
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2
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Joe H, Kim HG. Multi-label classification with XGBoost for metabolic pathway prediction. BMC Bioinformatics 2024; 25:52. [PMID: 38297220 PMCID: PMC10832249 DOI: 10.1186/s12859-024-05666-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 01/22/2024] [Indexed: 02/02/2024] Open
Abstract
BACKGROUND Metabolic pathway prediction is one possible approach to address the problem in system biology of reconstructing an organism's metabolic network from its genome sequence. Recently there have been developments in machine learning-based pathway prediction methods that conclude that machine learning-based approaches are similar in performance to the most used method, PathoLogic which is a rule-based method. One issue is that previous studies evaluated PathoLogic without taxonomic pruning which decreases its performance. RESULTS In this study, we update the evaluation results from previous studies to demonstrate that PathoLogic with taxonomic pruning outperforms previous machine learning-based approaches and that further improvements in performance need to be made for them to be competitive. Furthermore, we introduce mlXGPR, a XGBoost-based metabolic pathway prediction method based on the multi-label classification pathway prediction framework introduced from mlLGPR. We also improve on this multi-label framework by utilizing correlations between labels using classifier chains. We propose a ranking method that determines the order of the chain so that lower performing classifiers are placed later in the chain to utilize the correlations between labels more. We evaluate mlXGPR with and without classifier chains on single-organism and multi-organism benchmarks. Our results indicate that mlXGPR outperform other previous pathway prediction methods including PathoLogic with taxonomic pruning in terms of hamming loss, precision and F1 score on single organism benchmarks. CONCLUSIONS The results from our study indicate that the performance of machine learning-based pathway prediction methods can be substantially improved and can even outperform PathoLogic with taxonomic pruning.
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Affiliation(s)
- Hyunwhan Joe
- Biomedical Knowledge Engineering Lab., Seoul National University, Seoul, Republic of Korea
| | - Hong-Gee Kim
- Biomedical Knowledge Engineering Lab., Seoul National University, Seoul, Republic of Korea.
- School of Dentistry and Dental Research Institute, Seoul National University, Seoul, Republic of Korea.
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3
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Baker M, Zhang X, Maciel-Guerra A, Babaarslan K, Dong Y, Wang W, Hu Y, Renney D, Liu L, Li H, Hossain M, Heeb S, Tong Z, Pearcy N, Zhang M, Geng Y, Zhao L, Hao Z, Senin N, Chen J, Peng Z, Li F, Dottorini T. Convergence of resistance and evolutionary responses in Escherichia coli and Salmonella enterica co-inhabiting chicken farms in China. Nat Commun 2024; 15:206. [PMID: 38182559 PMCID: PMC10770378 DOI: 10.1038/s41467-023-44272-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 12/06/2023] [Indexed: 01/07/2024] Open
Abstract
Sharing of genetic elements among different pathogens and commensals inhabiting same hosts and environments has significant implications for antimicrobial resistance (AMR), especially in settings with high antimicrobial exposure. We analysed 661 Escherichia coli and Salmonella enterica isolates collected within and across hosts and environments, in 10 Chinese chicken farms over 2.5 years using data-mining methods. Most isolates within same hosts possessed the same clinically relevant AMR-carrying mobile genetic elements (plasmids: 70.6%, transposons: 78%), which also showed recent common evolution. Supervised machine learning classifiers revealed known and novel AMR-associated mutations and genes underlying resistance to 28 antimicrobials, primarily associated with resistance in E. coli and susceptibility in S. enterica. Many were essential and affected same metabolic processes in both species, albeit with varying degrees of phylogenetic penetration. Multi-modal strategies are crucial to investigate the interplay of mobilome, resistance and metabolism in cohabiting bacteria, especially in ecological settings where community-driven resistance selection occurs.
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Affiliation(s)
- Michelle Baker
- School of Veterinary Medicine and Science, University of Nottingham, College Road, Sutton Bonington, Loughborough, Leicestershire, LE12 5RD, UK
| | - Xibin Zhang
- Shandong New Hope Liuhe Group Co. Ltd. and Qingdao Key Laboratory of Animal Feed Safety, Qingdao, Shandong, 266000, P.R. China
| | - Alexandre Maciel-Guerra
- School of Veterinary Medicine and Science, University of Nottingham, College Road, Sutton Bonington, Loughborough, Leicestershire, LE12 5RD, UK
| | - Kubra Babaarslan
- School of Veterinary Medicine and Science, University of Nottingham, College Road, Sutton Bonington, Loughborough, Leicestershire, LE12 5RD, UK
| | - Yinping Dong
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, 100021, P. R. China
| | - Wei Wang
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, 100021, P. R. China
| | - Yujie Hu
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, 100021, P. R. China
| | - David Renney
- Nimrod Veterinary Products Limited, 2, Wychwood Court, Cotswold Business Village, Moreton-in-Marsh, GL56 0JQ, London, UK
| | - Longhai Liu
- Shandong Kaijia Food Co. Ltd, Weifang, P. R. China
| | - Hui Li
- Luoyang Center for Disease Control and Prevention, No. 9, Zhenghe Road, Luolong District, Luoyang City, Henan Province, Luolong, 471000, P. R. China
| | - Maqsud Hossain
- School of Veterinary Medicine and Science, University of Nottingham, College Road, Sutton Bonington, Loughborough, Leicestershire, LE12 5RD, UK
| | - Stephan Heeb
- School of Life Sciences, University of Nottingham, East Drive, Nottingham, Nottinghamshire, NG7 2RD, UK
| | - Zhiqin Tong
- Luoyang Center for Disease Control and Prevention, No. 9, Zhenghe Road, Luolong District, Luoyang City, Henan Province, Luolong, 471000, P. R. China
| | - Nicole Pearcy
- School of Veterinary Medicine and Science, University of Nottingham, College Road, Sutton Bonington, Loughborough, Leicestershire, LE12 5RD, UK
- School of Life Sciences, University of Nottingham, East Drive, Nottingham, Nottinghamshire, NG7 2RD, UK
| | - Meimei Zhang
- Liaoning Provincial Center for Disease Control and Prevention, No. 168, Jinfeng Street, Hunnan District, Shenyang City, Liaoning Province, 110072, P. R. China
| | - Yingzhi Geng
- Liaoning Provincial Center for Disease Control and Prevention, No. 168, Jinfeng Street, Hunnan District, Shenyang City, Liaoning Province, 110072, P. R. China
| | - Li Zhao
- Agricultural Biopharmaceutical Laboratory, College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, No. 700 Changcheng Road, Chengyang District, Qingdao City, Shandong Province, 266109, P. R. China
| | - Zhihui Hao
- Chinese Veterinary Medicine Innovation Center, College of Veterinary Medicine, China Agricultural University, Haidian District, Beijing City, 100193, P. R. China
| | - Nicola Senin
- Department of Engineering, University of Perugia, Perugia, I06125, Italy
| | - Junshi Chen
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, 100021, P. R. China
| | - Zixin Peng
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, 100021, P. R. China.
| | - Fengqin Li
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, 100021, P. R. China.
| | - Tania Dottorini
- School of Veterinary Medicine and Science, University of Nottingham, College Road, Sutton Bonington, Loughborough, Leicestershire, LE12 5RD, UK.
- Centre for Smart Food Research, Nottingham Ningbo China Beacons of Excellence Research and Innovation Institute, University of Nottingham Ningbo China, Ningbo, 315100, P. R. China.
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4
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Karp PD, Paley S, Caspi R, Kothari A, Krummenacker M, Midford PE, Moore LR, Subhraveti P, Gama-Castro S, Tierrafria VH, Lara P, Muñiz-Rascado L, Bonavides-Martinez C, Santos-Zavaleta A, Mackie A, Sun G, Ahn-Horst TA, Choi H, Covert MW, Collado-Vides J, Paulsen I. The EcoCyc Database (2023). EcoSal Plus 2023; 11:eesp00022023. [PMID: 37220074 PMCID: PMC10729931 DOI: 10.1128/ecosalplus.esp-0002-2023] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 04/04/2023] [Indexed: 01/28/2024]
Abstract
EcoCyc is a bioinformatics database available online at EcoCyc.org that describes the genome and the biochemical machinery of Escherichia coli K-12 MG1655. The long-term goal of the project is to describe the complete molecular catalog of the E. coli cell, as well as the functions of each of its molecular parts, to facilitate a system-level understanding of E. coli. EcoCyc is an electronic reference source for E. coli biologists and for biologists who work with related microorganisms. The database includes information pages on each E. coli gene product, metabolite, reaction, operon, and metabolic pathway. The database also includes information on the regulation of gene expression, E. coli gene essentiality, and nutrient conditions that do or do not support the growth of E. coli. The website and downloadable software contain tools for the analysis of high-throughput data sets. In addition, a steady-state metabolic flux model is generated from each new version of EcoCyc and can be executed online. The model can predict metabolic flux rates, nutrient uptake rates, and growth rates for different gene knockouts and nutrient conditions. Data generated from a whole-cell model that is parameterized from the latest data on EcoCyc are also available. This review outlines the data content of EcoCyc and of the procedures by which this content is generated.
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Affiliation(s)
- Peter D. Karp
- Bioinformatics Research Group, SRI International, Menlo Park, California, USA
| | - Suzanne Paley
- Bioinformatics Research Group, SRI International, Menlo Park, California, USA
| | - Ron Caspi
- Bioinformatics Research Group, SRI International, Menlo Park, California, USA
| | - Anamika Kothari
- Bioinformatics Research Group, SRI International, Menlo Park, California, USA
| | - Markus Krummenacker
- Bioinformatics Research Group, SRI International, Menlo Park, California, USA
| | - Peter E. Midford
- Bioinformatics Research Group, SRI International, Menlo Park, California, USA
| | - Lisa R. Moore
- Bioinformatics Research Group, SRI International, Menlo Park, California, USA
| | - Pallavi Subhraveti
- Bioinformatics Research Group, SRI International, Menlo Park, California, USA
| | - Socorro Gama-Castro
- Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Victor H. Tierrafria
- Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Paloma Lara
- Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Luis Muñiz-Rascado
- Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - César Bonavides-Martinez
- Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Alberto Santos-Zavaleta
- Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Amanda Mackie
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Gwanggyu Sun
- Department of Bioengineering, Stanford University, Stanford, California, USA
| | - Travis A. Ahn-Horst
- Department of Bioengineering, Stanford University, Stanford, California, USA
| | - Heejo Choi
- Department of Bioengineering, Stanford University, Stanford, California, USA
| | - Markus W. Covert
- Department of Bioengineering, Stanford University, Stanford, California, USA
| | - Julio Collado-Vides
- Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Ian Paulsen
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia
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5
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Belcour A, Got J, Aite M, Delage L, Collén J, Frioux C, Leblanc C, Dittami SM, Blanquart S, Markov GV, Siegel A. Inferring and comparing metabolism across heterogeneous sets of annotated genomes using AuCoMe. Genome Res 2023; 33:972-987. [PMID: 37468308 PMCID: PMC10629481 DOI: 10.1101/gr.277056.122] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 05/23/2023] [Indexed: 07/21/2023]
Abstract
Comparative analysis of genome-scale metabolic networks (GSMNs) may yield important information on the biology, evolution, and adaptation of species. However, it is impeded by the high heterogeneity of the quality and completeness of structural and functional genome annotations, which may bias the results of such comparisons. To address this issue, we developed AuCoMe, a pipeline to automatically reconstruct homogeneous GSMNs from a heterogeneous set of annotated genomes without discarding available manual annotations. We tested AuCoMe with three data sets, one bacterial, one fungal, and one algal, and showed that it successfully reduces technical biases while capturing the metabolic specificities of each organism. Our results also point out shared and divergent metabolic traits among evolutionarily distant algae, underlining the potential of AuCoMe to accelerate the broad exploration of metabolic evolution across the tree of life.
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Affiliation(s)
- Arnaud Belcour
- Univ Rennes, Inria, CNRS, IRISA, F-35000 Rennes, France;
| | - Jeanne Got
- Univ Rennes, Inria, CNRS, IRISA, F-35000 Rennes, France
| | - Méziane Aite
- Univ Rennes, Inria, CNRS, IRISA, F-35000 Rennes, France
| | - Ludovic Delage
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680 Roscoff, France
| | - Jonas Collén
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680 Roscoff, France
| | | | - Catherine Leblanc
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680 Roscoff, France
| | - Simon M Dittami
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680 Roscoff, France
| | | | - Gabriel V Markov
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680 Roscoff, France
| | - Anne Siegel
- Univ Rennes, Inria, CNRS, IRISA, F-35000 Rennes, France;
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6
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Ridone P, Ishida T, Lin A, Humphreys DT, Giannoulatou E, Sowa Y, Baker MAB. The rapid evolution of flagellar ion selectivity in experimental populations of E. coli. SCIENCE ADVANCES 2022; 8:eabq2492. [PMID: 36417540 PMCID: PMC9683732 DOI: 10.1126/sciadv.abq2492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 10/06/2022] [Indexed: 06/16/2023]
Abstract
Determining which cellular processes facilitate adaptation requires a tractable experimental model where an environmental cue can generate variants that rescue function. The bacterial flagellar motor (BFM) is an excellent candidate-an ancient and highly conserved molecular complex for bacterial propulsion toward favorable environments. Motor rotation is often powered by H+ or Na+ ion transit through the torque-generating stator subunit of the motor complex, and ion selectivity has adapted over evolutionary time scales. Here, we used CRISPR engineering to replace the native Escherichia coli H+-powered stator with Na+-powered stator genes and report the spontaneous reversion of our edit in a low-sodium environment. We followed the evolution of the stators during their reversion to H+-powered motility and used both whole-genome and RNA sequencing to identify genes involved in the cell's adaptation. Our transplant of an unfit protein and the cells' rapid response to this edit demonstrate the adaptability of the stator subunit and highlight the hierarchical modularity of the flagellar motor.
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Affiliation(s)
- Pietro Ridone
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Tsubasa Ishida
- Department of Frontier Bioscience, Hosei University, Tokyo, Japan
- Research Center for Micro-Nano Technology, Hosei University, Tokyo, Japan
| | - Angela Lin
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - David T. Humphreys
- Victor Chang Cardiac Research Institute, Sydney, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Australia
| | | | - Yoshiyuki Sowa
- Department of Frontier Bioscience, Hosei University, Tokyo, Japan
- Research Center for Micro-Nano Technology, Hosei University, Tokyo, Japan
| | - Matthew A. B. Baker
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
- ARC Centre of Excellence in Synthetic Biology, University of New South Wales, Sydney, Australia
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7
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Giuseppe A, Chiara P, Yun N, Igor J. Pathway integration and annotation: building a puzzle with non-matching pieces and no reference picture. Brief Bioinform 2022; 23:6691914. [PMID: 36063560 DOI: 10.1093/bib/bbac368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 07/25/2022] [Accepted: 08/05/2022] [Indexed: 11/13/2022] Open
Abstract
Biological pathways are a broadly used formalism for representing and interpreting the cascade of biochemical reactions underlying cellular and biological mechanisms. Pathway representation provides an ontological link among biomolecules such as RNA, DNA, small molecules, proteins, protein complexes, hormones and genes. Frequently, pathway annotations are used to identify mechanisms linked to genes within affected biological contexts. This important role and the simplicity and elegance in representing complex interactions led to an explosion of pathway representations and databases. Unfortunately, the lack of overlap across databases results in inconsistent enrichment analysis results, unless databases are integrated. However, due to absence of consensus, guidelines or gold standards in pathway definition and representation, integration of data across pathway databases is not straightforward. Despite multiple attempts to provide consolidated pathways, highly related, redundant, poorly overlapping or ambiguous pathways continue to render pathways analysis inconsistent and hard to interpret. Ontology-based integration will promote unbiased, comprehensive yet streamlined analysis of experiments, and will reduce the number of enriched pathways when performing pathway enrichment analysis. Moreover, appropriate and consolidated pathways provide better training data for pathway prediction algorithms. In this manuscript, we describe the current methods for pathway consolidation, their strengths and pitfalls, and highlight directions for future improvements to this research area.
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Affiliation(s)
- Agapito Giuseppe
- Department of Law, Economics and Social Sciences, University Magna Græcia of Catanzaro, Italy.,Data Analytic Research Center, University Magna Græcia of Catanzaro, Italy
| | - Pastrello Chiara
- Osteoarthritis Research Program, Division of Orthopaedics, Schroeder Arthritis Institute, University Health Network, Toronto, Canada
| | - Niu Yun
- Osteoarthritis Research Program, Division of Orthopaedics, Schroeder Arthritis Institute, University Health Network, Toronto, Canada
| | - Jurisica Igor
- Osteoarthritis Research Program, Division of Orthopaedics, Schroeder Arthritis Institute, University Health Network, Toronto, Canada.,Departments of Medical Biophysics and Computer Science Canada, University of Toronto, Toronto, Canada.,Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, Toronto, Canada.,Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia
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8
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Proteomic Profiling of Outer Membrane Vesicles Released by Escherichia coli LPS Mutants Defective in Heptose Biosynthesis. J Pers Med 2022; 12:jpm12081301. [PMID: 36013250 PMCID: PMC9410366 DOI: 10.3390/jpm12081301] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 08/03/2022] [Accepted: 08/08/2022] [Indexed: 11/17/2022] Open
Abstract
Escherichia coli releases outer membrane vesicles (OMVs) into the extracellular environment. OMVs, which contain the outer membrane protein, lipopolysaccharides (LPS), and genetic material, play an important role in immune response modulation. An isobaric tag for relative and absolute quantitation (iTRAQ) analysis was used to investigate OMV constituent proteins and their functions in burn trauma. OMV sizes ranged from 50 to 200 nm. Proteomics and Gene Ontology analysis revealed that ΔrfaC and ΔrfaG were likely involved in the upregulation of the structural constituent of ribosomes for the outer membrane and of proteins involved in protein binding and OMV synthesis. ΔrfaL was likely implicated in the downregulation of the structural constituent of the ribosome, translation, and cytosolic large ribosomal subunit. Kyoto Encyclopedia of Genes and Genomes analysis indicated that ΔrfaC and ΔrfaG downregulated ACP, ACEF, and ADHE genes; ΔrfaL upregulated ACP, ACEF, and ADHE genes. Heat map analysis demonstrated upregulation of galF, clpX, accA, fabB, and grpE and downregulation of pspA, ydiY, rpsT, and rpmB. These results suggest that RfaC, RfaG, and RfaL proteins were involved in outer membrane and LPS synthesis. Therefore, direct contact between wounds and LPS may lead to apoptosis, reduction in local cell proliferation, and delayed wound healing.
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9
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Shanbhag AP, Ghatak A, Rajagopal S. Industrial light at the end of the Iron-containing (group III) alcohol dehydrogenase tunnel. Biotechnol Appl Biochem 2022; 70:537-552. [PMID: 35751426 DOI: 10.1002/bab.2376] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 06/10/2022] [Indexed: 11/05/2022]
Abstract
There are three prominent alcohol dehydrogenases superfamilies: Short-chain, Medium-chain, and Iron-containing alcohol dehydrogenases (FeADHs). Many members are valuable catalysts for producing industrially relevant products such as Active pharmaceutical Intermediates, Chiral synthons, Biopolymers, Biofuels and secondary metabolites. However, FeADHs are the least explored enzymes among the superfamilies for commercial tenacities. They portray a conserved structure having a 'tunnel-like' cofactor and substrate binding site with particular functions, despite representing high sequence diversity. Interestingly, phylogenetic analysis demarcates enzymes catalyzing distinct native substrates where closely related clades convert similar molecules. Further, homologs from various mesophilic and thermophilic microbes have been explored for designing a solvent and temperature resistant enzyme for industrial purposes. The review explores different Iron-containing alcohol dehydrogenases potential engineering of the enzymes and substrates helpful in manufacturing commercial products. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Anirudh P Shanbhag
- Bugworks Research India Pvt. Ltd., C-CAMP, National Centre for Biological Sciences (NCBS), UAS GKVK Campus, Bangalore, 560065.,Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, 700009, India
| | - Arindam Ghatak
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, 700009, India.,Biomoneta Research Pvt. Ltd., C-CAMP, National Centre for Biological Sciences (NCBS), UAS GKVK Campus, Bangalore, 560065
| | - Sreenath Rajagopal
- Bugworks Research India Pvt. Ltd., C-CAMP, National Centre for Biological Sciences (NCBS), UAS GKVK Campus, Bangalore, 560065
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10
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A genome-scale metabolic model of Cupriavidus necator H16 integrated with TraDIS and transcriptomic data reveals metabolic insights for biotechnological applications. PLoS Comput Biol 2022; 18:e1010106. [PMID: 35604933 PMCID: PMC9166356 DOI: 10.1371/journal.pcbi.1010106] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 06/03/2022] [Accepted: 04/14/2022] [Indexed: 11/29/2022] Open
Abstract
Exploiting biological processes to recycle renewable carbon into high value platform chemicals provides a sustainable and greener alternative to current reliance on petrochemicals. In this regard Cupriavidus necator H16 represents a particularly promising microbial chassis due to its ability to grow on a wide range of low-cost feedstocks, including the waste gas carbon dioxide, whilst also naturally producing large quantities of polyhydroxybutyrate (PHB) during nutrient-limited conditions. Understanding the complex metabolic behaviour of this bacterium is a prerequisite for the design of successful engineering strategies for optimising product yields. We present a genome-scale metabolic model (GSM) of C. necator H16 (denoted iCN1361), which is directly constructed from the BioCyc database to improve the readability and reusability of the model. After the initial automated construction, we have performed extensive curation and both theoretical and experimental validation. By carrying out a genome-wide essentiality screening using a Transposon-directed Insertion site Sequencing (TraDIS) approach, we showed that the model could predict gene knockout phenotypes with a high level of accuracy. Importantly, we indicate how experimental and computational predictions can be used to improve model structure and, thus, model accuracy as well as to evaluate potential false positives identified in the experiments. Finally, by integrating transcriptomics data with iCN1361 we create a condition-specific model, which, importantly, better reflects PHB production in C. necator H16. Observed changes in the omics data and in-silico-estimated alterations in fluxes were then used to predict the regulatory control of key cellular processes. The results presented demonstrate that iCN1361 is a valuable tool for unravelling the system-level metabolic behaviour of C. necator H16 and can provide useful insights for designing metabolic engineering strategies. Genome-scale metabolic models (GSMs) provide a tool for unravelling the complex metabolic behaviour of bacteria and how they adapt to changing environments and genetic perturbations, and thus offer invaluable insights for biotechnology applications. For a GSM to be used efficiently for strain development purposes, however, the model must be easily readable and reusable by other researchers, whilst being able to predict metabolic behaviour with a high level of accuracy. In this work, we developed a GSM for Cupriavidus necator H16 that is linked to the BioCyc database, which provides an efficient way of application, model update, integration of experimental data and network visualisation for other researchers. Using our model, we demonstrate how integrating experimental observations, including Transposon-directed Insertion site Sequencing (TraDIS) and omics data, can be used to compensate for the lack of regulatory, kinetic and thermodynamic information in GSMs, and thus improve model accuracy. Importantly, we found that TraDIS in vivo screening and GSM analysis are complementary approaches, which can be used in combination to provide reliable gene essentiality predictions. Overall, our results offer an informed strategy for the deliberate manipulation of C. necator H16 metabolic capabilities, towards its industrial application to convert greenhouse gases into biochemicals and biofuels.
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Liu S, Moon CD, Zheng N, Huws S, Zhao S, Wang J. Opportunities and challenges of using metagenomic data to bring uncultured microbes into cultivation. MICROBIOME 2022; 10:76. [PMID: 35546409 PMCID: PMC9097414 DOI: 10.1186/s40168-022-01272-5] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 04/10/2022] [Indexed: 05/12/2023]
Abstract
Although there is now an extensive understanding of the diversity of microbial life on earth through culture-independent metagenomic DNA sequence analyses, the isolation and cultivation of microbes remains critical to directly study them and confirm their metabolic and physiological functions, and their ecological roles. The majority of environmental microbes are as yet uncultured however; therefore, bringing these rare or poorly characterized groups into culture is a priority to further understand microbiome functions. Moreover, cultivated isolates may find utility in a range of applications, such as new probiotics, biocontrol agents, and agents for industrial processes. The growing abundance of metagenomic and meta-transcriptomic sequence information from a wide range of environments provides more opportunities to guide the isolation and cultivation of microbes of interest. In this paper, we discuss a range of successful methodologies and applications that have underpinned recent metagenome-guided isolation and cultivation of microbe efforts. These approaches include determining specific culture conditions to enrich for taxa of interest, to more complex strategies that specifically target the capture of microbial species through antibody engineering and genome editing strategies. With the greater degree of genomic information now available from uncultivated members, such as via metagenome-assembled genomes, the theoretical understanding of their cultivation requirements will enable greater possibilities to capture these and ultimately gain a more comprehensive understanding of the microbiomes. Video Abstract.
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Affiliation(s)
- Sijia Liu
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Haidian, Beijing, 100193, China
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Christina D Moon
- AgResearch Ltd., Grasslands Research Centre, Palmerston North, New Zealand
| | - Nan Zheng
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Haidian, Beijing, 100193, China
| | - Sharon Huws
- School of Biological Sciences and Institute for Global Food Security, 19 Chlorine Gardens, Queen's University Belfast, Belfast, UK
| | - Shengguo Zhao
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Haidian, Beijing, 100193, China.
| | - Jiaqi Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Haidian, Beijing, 100193, China.
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Dhyani R, Jain S, Bhatt A, Kumar P, Navani NK. Genetic regulatory element based whole-cell biosensors for the detection of metabolic disorders. Biosens Bioelectron 2021; 199:113869. [PMID: 34915213 DOI: 10.1016/j.bios.2021.113869] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 12/03/2021] [Accepted: 12/05/2021] [Indexed: 11/29/2022]
Abstract
Clinicians require simple, and cost-effective diagnostic tools for the quantitative determination of amino acids in physiological fluids for the detection of metabolic disorder diseases. Besides, amino acids also act as biological markers for different types of cancers and cardiovascular diseases. Herein, we applied an in-silico based approach to identify potential amino acid-responsive genetic regulatory elements for the detection of metabolic disorders in humans. Identified sequences were further transcriptionally fused with GFP, thus generating an optical readout in response to their cognate targets. Screening of genetic regulatory elements led us to discover two promoter elements (pmetE::GFP and ptrpL::GFP) that showed a significant change in the fluorescence response to homocysteine and tryptophan, respectively. The developed biosensors respond specifically and sensitively with a limit of detection of 3.8 μM and 3 μM for homocysteine and tryptophan, respectively. Furthermore, the clinical utility of this assay was demonstrated by employing it to identify homocystinuria and tryptophanuria diseases through the quantification of homocysteine and tryptophan in plasma and urine samples within 5 h. The precision and accuracy of the biosensors for disease diagnosis were well within an acceptable range. The general strategy used in this system can be expanded to screen different genetic regulatory elements present in other gram-negative and gram-positive bacteria for the detection of metabolic disorders.
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Affiliation(s)
- Rajat Dhyani
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, Uttarakhand, 247667, India
| | - Shubham Jain
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, Uttarakhand, 247667, India
| | - Ankita Bhatt
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, Uttarakhand, 247667, India
| | - Piyush Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, Uttarakhand, 247667, India
| | - Naveen Kumar Navani
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, Uttarakhand, 247667, India.
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Genome-Scale Metabolic Models and Machine Learning Reveal Genetic Determinants of Antibiotic Resistance in Escherichia coli and Unravel the Underlying Metabolic Adaptation Mechanisms. mSystems 2021; 6:e0091320. [PMID: 34342537 PMCID: PMC8409726 DOI: 10.1128/msystems.00913-20] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Antimicrobial resistance (AMR) is becoming one of the largest threats to public health worldwide, with the opportunistic pathogen Escherichia coli playing a major role in the AMR global health crisis. Unravelling the complex interplay between drug resistance and metabolic rewiring is key to understand the ability of bacteria to adapt to new treatments and to the development of new effective solutions to combat resistant infections. We developed a computational pipeline that combines machine learning with genome-scale metabolic models (GSMs) to elucidate the systemic relationships between genetic determinants of resistance and metabolism beyond annotated drug resistance genes. Our approach was used to identify genetic determinants of 12 AMR profiles for the opportunistic pathogenic bacterium E. coli. Then, to interpret the large number of identified genetic determinants, we applied a constraint-based approach using the GSM to predict the effects of genetic changes on growth, metabolite yields, and reaction fluxes. Our computational platform leads to multiple results. First, our approach corroborates 225 known AMR-conferring genes, 35 of which are known for the specific antibiotic. Second, integration with the GSM predicted 20 top-ranked genetic determinants (including accA, metK, fabD, fabG, murG, lptG, mraY, folP, and glmM) essential for growth, while a further 17 top-ranked genetic determinants linked AMR to auxotrophic behavior. Third, clusters of AMR-conferring genes affecting similar metabolic processes are revealed, which strongly suggested that metabolic adaptations in cell wall, energy, iron and nucleotide metabolism are associated with AMR. The computational solution can be used to study other human and animal pathogens. IMPORTANCEEscherichia coli is a major public health concern given its increasing level of antibiotic resistance worldwide and extraordinary capacity to acquire and spread resistance via horizontal gene transfer with surrounding species and via mutations in its existing genome. E. coli also exhibits a large amount of metabolic pathway redundancy, which promotes resistance via metabolic adaptability. In this study, we developed a computational approach that integrates machine learning with metabolic modeling to understand the correlation between AMR and metabolic adaptation mechanisms in this model bacterium. Using our approach, we identified AMR genetic determinants associated with cell wall modifications for increased permeability, virulence factor manipulation of host immunity, reduction of oxidative stress toxicity, and changes to energy metabolism. Unravelling the complex interplay between antibiotic resistance and metabolic rewiring may open new opportunities to understand the ability of E. coli, and potentially of other human and animal pathogens, to adapt to new treatments.
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Shah HA, Liu J, Yang Z, Feng J. Review of Machine Learning Methods for the Prediction and Reconstruction of Metabolic Pathways. Front Mol Biosci 2021; 8:634141. [PMID: 34222327 PMCID: PMC8247443 DOI: 10.3389/fmolb.2021.634141] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 06/01/2021] [Indexed: 11/13/2022] Open
Abstract
Prediction and reconstruction of metabolic pathways play significant roles in many fields such as genetic engineering, metabolic engineering, drug discovery, and are becoming the most active research topics in synthetic biology. With the increase of related data and with the development of machine learning techniques, there have many machine leaning based methods been proposed for prediction or reconstruction of metabolic pathways. Machine learning techniques are showing state-of-the-art performance to handle the rapidly increasing volume of data in synthetic biology. To support researchers in this field, we briefly review the research progress of metabolic pathway reconstruction and prediction based on machine learning. Some challenging issues in the reconstruction of metabolic pathways are also discussed in this paper.
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Affiliation(s)
- Hayat Ali Shah
- Institute of Artificial Intelligence, School of Computer Science, Wuhan University, Wuhan, China
| | - Juan Liu
- Institute of Artificial Intelligence, School of Computer Science, Wuhan University, Wuhan, China
| | - Zhihui Yang
- Institute of Artificial Intelligence, School of Computer Science, Wuhan University, Wuhan, China
| | - Jing Feng
- Institute of Artificial Intelligence, School of Computer Science, Wuhan University, Wuhan, China
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Murata M, Nakamura K, Kosaka T, Ota N, Osawa A, Muro R, Fujiyama K, Oshima T, Mori H, Wanner BL, Yamada M. Cell Lysis Directed by SulA in Response to DNA Damage in Escherichia coli. Int J Mol Sci 2021; 22:ijms22094535. [PMID: 33926096 PMCID: PMC8123628 DOI: 10.3390/ijms22094535] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/21/2021] [Accepted: 04/21/2021] [Indexed: 11/24/2022] Open
Abstract
The SOS response is induced upon DNA damage and the inhibition of Z ring formation by the product of the sulA gene, which is one of the LexA-regulated genes, allows time for repair of damaged DNA. On the other hand, severely DNA-damaged cells are eliminated from cell populations. Overexpression of sulA leads to cell lysis, suggesting SulA eliminates cells with unrepaired damaged DNA. Transcriptome analysis revealed that overexpression of sulA leads to up-regulation of numerous genes, including soxS. Deletion of soxS markedly reduced the extent of cell lysis by sulA overexpression and soxS overexpression alone led to cell lysis. Further experiments on the SoxS regulon suggested that LpxC is a main player downstream from SoxS. These findings suggested the SulA-dependent cell lysis (SDCL) cascade as follows: SulA→SoxS→LpxC. Other tests showed that the SDCL cascade pathway does not overlap with the apoptosis-like and mazEF cell death pathways.
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Affiliation(s)
- Masayuki Murata
- Life Science, Graduate School of Science and Technology for Innovation, Yamaguchi University, Ube 755-8611, Japan; (M.M.); (T.K.); (N.O.); (A.O.)
| | - Keiko Nakamura
- Applied Molecular Bioscience, Graduate School of Medicine, Yamaguchi University, Ube 755-8505, Japan; (K.N.); (R.M.); (K.F.)
| | - Tomoyuki Kosaka
- Life Science, Graduate School of Science and Technology for Innovation, Yamaguchi University, Ube 755-8611, Japan; (M.M.); (T.K.); (N.O.); (A.O.)
- Research Center for Thermotolerant Microbial Resources, Yamaguchi University, Yamaguchi 753-8515, Japan
| | - Natsuko Ota
- Life Science, Graduate School of Science and Technology for Innovation, Yamaguchi University, Ube 755-8611, Japan; (M.M.); (T.K.); (N.O.); (A.O.)
| | - Ayumi Osawa
- Life Science, Graduate School of Science and Technology for Innovation, Yamaguchi University, Ube 755-8611, Japan; (M.M.); (T.K.); (N.O.); (A.O.)
| | - Ryunosuke Muro
- Applied Molecular Bioscience, Graduate School of Medicine, Yamaguchi University, Ube 755-8505, Japan; (K.N.); (R.M.); (K.F.)
| | - Kazuya Fujiyama
- Applied Molecular Bioscience, Graduate School of Medicine, Yamaguchi University, Ube 755-8505, Japan; (K.N.); (R.M.); (K.F.)
| | - Taku Oshima
- Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan;
| | - Hirotada Mori
- Graduate School of Information Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan;
| | - Barry L. Wanner
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA;
| | - Mamoru Yamada
- Life Science, Graduate School of Science and Technology for Innovation, Yamaguchi University, Ube 755-8611, Japan; (M.M.); (T.K.); (N.O.); (A.O.)
- Applied Molecular Bioscience, Graduate School of Medicine, Yamaguchi University, Ube 755-8505, Japan; (K.N.); (R.M.); (K.F.)
- Research Center for Thermotolerant Microbial Resources, Yamaguchi University, Yamaguchi 753-8515, Japan
- Correspondence: ; Tel.: +81-83-933-5869
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Heiden SE, Hübner NO, Bohnert JA, Heidecke CD, Kramer A, Balau V, Gierer W, Schaefer S, Eckmanns T, Gatermann S, Eger E, Guenther S, Becker K, Schaufler K. A Klebsiella pneumoniae ST307 outbreak clone from Germany demonstrates features of extensive drug resistance, hypermucoviscosity, and enhanced iron acquisition. Genome Med 2020; 12:113. [PMID: 33298160 PMCID: PMC7724794 DOI: 10.1186/s13073-020-00814-6] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 11/25/2020] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Antibiotic-resistant Klebsiella pneumoniae are a major cause of hospital- and community-acquired infections, including sepsis, liver abscess, and pneumonia, driven mainly by the emergence of successful high-risk clonal lineages. The K. pneumoniae sequence type (ST) 307 lineage has appeared in several different parts of the world after first being described in Europe in 2008. From June to October 2019, we recorded an outbreak of an extensively drug-resistant ST307 lineage in four medical facilities in north-eastern Germany. METHODS Here, we investigated these isolates and those from subsequent cases in the same facilities. We performed whole-genome sequencing to study phylogenetics, microevolution, and plasmid transmission, as well as phenotypic experiments including growth curves, hypermucoviscosity, siderophore secretion, biofilm formation, desiccation resilience, serum survival, and heavy metal resistance for an in-depth characterization of this outbreak clone. RESULTS Phylogenetics suggest a homogenous phylogram with several sub-clades containing either isolates from only one patient or isolates originating from different patients, suggesting inter-patient transmission. We identified three large resistance plasmids, carrying either NDM-1, CTX-M-15, or OXA-48, which K. pneumoniae ST307 likely donated to other K. pneumoniae isolates of different STs and even other bacterial species (e.g., Enterobacter cloacae) within the clinical settings. Several chromosomally and plasmid-encoded, hypervirulence-associated virulence factors (e.g., yersiniabactin, metabolite transporter, aerobactin, and heavy metal resistance genes) were identified in addition. While growth, biofilm formation, desiccation resilience, serum survival, and heavy metal resistance were comparable to several control strains, results from siderophore secretion and hypermucoviscosity experiments revealed superiority of the ST307 clone, similar to an archetypical, hypervirulent K. pneumoniae strain (hvKP1). CONCLUSIONS The combination of extensive drug resistance and virulence, partly conferred through a "mosaic" plasmid carrying both antibiotic resistance and hypervirulence-associated features, demonstrates serious public health implications.
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Affiliation(s)
- Stefan E Heiden
- Institute of Pharmacy, Pharmaceutical Microbiology, University of Greifswald, Friedrich-Ludwig-Jahn-Str. 17, 17489, Greifswald, Germany
| | - Nils-Olaf Hübner
- Central Unit for Infection Prevention and Control, University Medicine Greifswald, Greifswald, Germany
| | - Jürgen A Bohnert
- Friedrich Loeffler-Institute of Medical Microbiology, University Medicine Greifswald, Greifswald, Germany
| | - Claus-Dieter Heidecke
- Department of General, Visceral, Thoracic and Vascular Surgery, University Medicine Greifswald, Greifswald, Germany
| | - Axel Kramer
- Institute for Hygiene and Environmental Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Veronika Balau
- IMD Laboratory Greifswald, Institute of Medical Diagnostics, Greifswald, Germany
| | | | | | - Tim Eckmanns
- Department for Infectious Disease Epidemiology, Robert Koch-Institute, Berlin, Germany
| | - Sören Gatermann
- National Reference Centre for Multidrug-Resistant Gram-Negative Bacteria, Ruhr University Bochum, Bochum, Germany
| | - Elias Eger
- Institute of Pharmacy, Pharmaceutical Microbiology, University of Greifswald, Friedrich-Ludwig-Jahn-Str. 17, 17489, Greifswald, Germany
| | - Sebastian Guenther
- Institute of Pharmacy, Pharmaceutical Biology, University of Greifswald, Greifswald, Germany
| | - Karsten Becker
- Friedrich Loeffler-Institute of Medical Microbiology, University Medicine Greifswald, Greifswald, Germany
| | - Katharina Schaufler
- Institute of Pharmacy, Pharmaceutical Microbiology, University of Greifswald, Friedrich-Ludwig-Jahn-Str. 17, 17489, Greifswald, Germany.
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Quantifying the distribution of protein oligomerization degree reflects cellular information capacity. Sci Rep 2020; 10:17689. [PMID: 33077848 PMCID: PMC7573690 DOI: 10.1038/s41598-020-74811-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Accepted: 09/29/2020] [Indexed: 11/08/2022] Open
Abstract
The generation of information, energy and biomass in living cells involves integrated processes that optimally evolve into complex and robust cellular networks. Protein homo-oligomerization, which is correlated with cooperativity in biology, is one means of scaling the complexity of protein networks. It can play critical roles in determining the sensitivity of genetic regulatory circuits and metabolic pathways. Therefore, understanding the roles of oligomerization may lead to new approaches of probing biological functions. Here, we analyzed the frequency of protein oligomerization degree in the cell proteome of nine different organisms, and then, we asked whether there are design trade-offs between protein oligomerization, information precision and energy costs of protein synthesis. Our results indicate that there is an upper limit for the degree of protein oligomerization, possibly because of the trade-off between cellular resource limitations and the information precision involved in biochemical reaction networks. These findings can explain the principles of cellular architecture design and provide a quantitative tool to scale synthetic biological systems.
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Soh SM, Jang H, Mitchell RJ. Loss of the lipopolysaccharide (LPS) inner core increases the electrocompetence of Escherichia coli. Appl Microbiol Biotechnol 2020; 104:7427-7435. [PMID: 32676713 DOI: 10.1007/s00253-020-10779-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 06/28/2020] [Accepted: 07/05/2020] [Indexed: 12/19/2022]
Abstract
Mutations that shorten the lipopolysaccharide (LPS) in Escherichia coli were found to significantly increase the number of transformants after electroporation. The loss of the LPS outer core increased the number of transformants with plasmid pAmCyan (3.3 kb) from 5.0 × 105 colony-forming units (CFU)/μg in the wild-type E. coli BW25113 to 3.3 × 107 CFU/μg in a ΔwaaG background, a 66.2-fold increase in efficiency. Truncation of the inner core improved this even further, with the ΔwaaF mutant exhibiting the best transformation efficiencies obtained, i.e., a 454.7-fold increase in the number of colonies over the wild-type strain. Similar results were obtained when a larger plasmid (pDA1; 11.3 kb) was used, with the ΔwaaF mutant once more giving the best transformation rates, i.e., a 73.7-fold increase. Subsequent tests proved that the enhanced transformabilities of these mutants were not due to a better survival or their surface charge properties, nor from preferential binding of these strains to the plasmid. Using N-phenyl-1-naphthylamine (NPN), we confirmed that the outer membranes of these mutant strains were more permeable. We also found that they leaked more ATP (3.4- and 2.0-fold higher for the ΔwaaF and ΔwaaG mutants, respectively, than wild-type E. coli BW25113), suggesting that the inner membrane stability is also reduced, helping to explain how the DNA enters these cells more easily. KEY POINTS: • LPS inner core gene knockouts increase the electrocompetence of E. coli. • No significant difference in survival, surface charge, or DNA binding was evident. • The LPS inner core mutants, however, exhibited higher outer membrane permeability. • Their inner membranes were also leaky, based on supernatant ATP concentrations.
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Affiliation(s)
- Sandrine M Soh
- School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, South Korea
| | - Hyochan Jang
- School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, South Korea
| | - Robert J Mitchell
- School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, South Korea.
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De Las Rivas J, Bonavides-Martínez C, Campos-Laborie FJ. Bioinformatics in Latin America and SoIBio impact, a tale of spin-off and expansion around genomes and protein structures. Brief Bioinform 2019; 20:390-397. [PMID: 28981567 PMCID: PMC6433739 DOI: 10.1093/bib/bbx064] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 04/18/2017] [Indexed: 11/30/2022] Open
Abstract
Owing to the emerging impact of bioinformatics and computational biology, in this article, we present an overview of the history and current state of the research on this field in Latin America (LA). It will be difficult to cover without inequality all the efforts, initiatives and works that have happened for the past two decades in this vast region (that includes >19 million km2 and >600 million people). Despite the difficulty, we have done an analytical search looking for publications in the field made by researchers from 19 LA countries in the past 25 years. In this way, we find that research in bioinformatics in this region should develop twice to approach the average world scientific production in the field. We also found some of the pioneering scientists who initiated and led bioinformatics in the region and were promoters of this new scientific field. Our analysis also reveals that spin-off began around some specific areas within the biomolecular sciences: studies on genomes (anchored in the new generation of deep sequencing technologies, followed by developments in proteomics) and studies on protein structures (supported by three-dimensional structural determination technologies and their computational advancement). Finally, we show that the contribution to this endeavour of the Iberoamerican Society for Bioinformatics, founded in Mexico in 2009, has been significant, as it is a leading forum to join efforts of many scientists from LA interested in promoting research, training and education in bioinformatics.
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Affiliation(s)
- Javier De Las Rivas
- CSIC and Universidad de Salamanca, Bioinformatics and Functional Genomics Group, Cancer Research Center (IMBCC, CSIC/USAL/IBSAL), Salamanca, Spain
- Corresponding author. Javier De Las Rivas, Bioinformatics and Functional Genomics Group, Cancer Research Center (IMBCC, CSIC/USAL/IBSAL), Consejo Superior de Investigaciones Científicas (CSIC) and Universidad de Salamanca (USAL), Campus Miguel de Unamuno s/n, Salamanca 37007, Spain. Tel.: +34 923294819; Fax: +34923294743; E-mail:
| | - Cesar Bonavides-Martínez
- Universidad Nacional Autonoma de Mexico, Computational Genomics, Centro de Ciencias Genómicas, Cuernavaca, Morelos, Mexico
| | - Francisco Jose Campos-Laborie
- CSIC and Universidad de Salamanca, Bioinformatics and Functional Genomics Group, Cancer Research Center (IMBCC, CSIC/USAL/IBSAL), Salamanca, Spain
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Lee YJ, Kim SJ, Amrofell MB, Moon TS. Establishing a Multivariate Model for Predictable Antisense RNA-Mediated Repression. ACS Synth Biol 2019; 8:45-56. [PMID: 30517781 DOI: 10.1021/acssynbio.8b00227] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Recent advances in our understanding of RNA folding and functions have facilitated the use of regulatory RNAs such as synthetic antisense RNAs (asRNAs) to modulate gene expression. However, despite the simple and universal complementarity rule, predictable asRNA-mediated repression is still challenging due to the intrinsic complexity of native asRNA-mediated gene regulation. To address this issue, we present a multivariate model, based on the change in free energy of complex formation (Δ GCF) and percent mismatch of the target binding region, which can predict synthetic asRNA-mediated repression efficiency in diverse contexts. First, 69 asRNAs that bind to multiple target mRNAs were designed and tested to create the predictive model. Second, we showed that the same model is effective predicting repression of target genes in both plasmids and chromosomes. Third, using our model, we designed asRNAs that simultaneously modulated expression of a toxin and its antitoxin to demonstrate tunable control of cell growth. Fourth, we tested and validated the same model in two different biotechnologically important organisms: Escherichia coli Nissle 1917 and Bacillus subtilis 168. Last, multiple parameters, including target locations, the presence of an Hfq binding site, GC contents, and gene expression levels, were revisited to define the conditions under which the multivariate model should be used for accurate prediction. Together, 434 different strain-asRNA combinations were tested, validating the predictive model in a variety of contexts, including multiple target genes and organisms. The result presented in this study is an important step toward achieving predictable tunability of asRNA-mediated repression.
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Affiliation(s)
- Young Je Lee
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Soo-Jung Kim
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Matthew B. Amrofell
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Tae Seok Moon
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
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21
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Karp PD, Ong WK, Paley S, Billington R, Caspi R, Fulcher C, Kothari A, Krummenacker M, Latendresse M, Midford PE, Subhraveti P, Gama-Castro S, Muñiz-Rascado L, Bonavides-Martinez C, Santos-Zavaleta A, Mackie A, Collado-Vides J, Keseler IM, Paulsen I. The EcoCyc Database. EcoSal Plus 2018; 8:10.1128/ecosalplus.ESP-0006-2018. [PMID: 30406744 PMCID: PMC6504970 DOI: 10.1128/ecosalplus.esp-0006-2018] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Indexed: 01/28/2023]
Abstract
EcoCyc is a bioinformatics database available at EcoCyc.org that describes the genome and the biochemical machinery of Escherichia coli K-12 MG1655. The long-term goal of the project is to describe the complete molecular catalog of the E. coli cell, as well as the functions of each of its molecular parts, to facilitate a system-level understanding of E. coli. EcoCyc is an electronic reference source for E. coli biologists and for biologists who work with related microorganisms. The database includes information pages on each E. coli gene product, metabolite, reaction, operon, and metabolic pathway. The database also includes information on E. coli gene essentiality and on nutrient conditions that do or do not support the growth of E. coli. The website and downloadable software contain tools for analysis of high-throughput data sets. In addition, a steady-state metabolic flux model is generated from each new version of EcoCyc and can be executed via EcoCyc.org. The model can predict metabolic flux rates, nutrient uptake rates, and growth rates for different gene knockouts and nutrient conditions. This review outlines the data content of EcoCyc and of the procedures by which this content is generated.
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Affiliation(s)
- Peter D Karp
- Bioinformatics Research Group, SRI International, Menlo Park, CA 94025
| | - Wai Kit Ong
- Bioinformatics Research Group, SRI International, Menlo Park, CA 94025
| | - Suzanne Paley
- Bioinformatics Research Group, SRI International, Menlo Park, CA 94025
| | | | - Ron Caspi
- Bioinformatics Research Group, SRI International, Menlo Park, CA 94025
| | - Carol Fulcher
- Bioinformatics Research Group, SRI International, Menlo Park, CA 94025
| | - Anamika Kothari
- Bioinformatics Research Group, SRI International, Menlo Park, CA 94025
| | | | - Mario Latendresse
- Bioinformatics Research Group, SRI International, Menlo Park, CA 94025
| | - Peter E Midford
- Bioinformatics Research Group, SRI International, Menlo Park, CA 94025
| | | | - Socorro Gama-Castro
- Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, A.P. 565-A, Cuernavaca, Morelos 62100, México
| | - Luis Muñiz-Rascado
- Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, A.P. 565-A, Cuernavaca, Morelos 62100, México
| | - César Bonavides-Martinez
- Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, A.P. 565-A, Cuernavaca, Morelos 62100, México
| | - Alberto Santos-Zavaleta
- Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, A.P. 565-A, Cuernavaca, Morelos 62100, México
| | - Amanda Mackie
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Julio Collado-Vides
- Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, A.P. 565-A, Cuernavaca, Morelos 62100, México
| | - Ingrid M Keseler
- Bioinformatics Research Group, SRI International, Menlo Park, CA 94025
| | - Ian Paulsen
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
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22
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Methods for automated genome-scale metabolic model reconstruction. Biochem Soc Trans 2018; 46:931-936. [PMID: 30065105 DOI: 10.1042/bst20170246] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 06/04/2018] [Accepted: 06/06/2018] [Indexed: 11/17/2022]
Abstract
In the era of next-generation sequencing and ubiquitous assembly and binning of metagenomes, new putative genome sequences are being produced from isolate and microbiome samples at ever-increasing rates. Genome-scale metabolic models have enormous utility for supporting the analysis and predictive characterization of these genomes based on sequence data. As a result, tools for rapid automated reconstruction of metabolic models are becoming critically important for supporting the analysis of new genome sequences. Many tools and algorithms have now emerged to support rapid model reconstruction and analysis. Here, we are comparing and contrasting the capabilities and output of a variety of these tools, including ModelSEED, Raven Toolbox, PathwayTools, SuBliMinal Toolbox and merlin.
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23
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Edirisinghe JN, Faria JP, Harris NL, Allen BH, Henry CS. Reconstruction and Analysis of Central Metabolism in Microbes. Methods Mol Biol 2018; 1716:111-129. [PMID: 29222751 DOI: 10.1007/978-1-4939-7528-0_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Genome-scale metabolic models (GEMs) generated from automated reconstruction pipelines often lack accuracy due to the need for extensive gapfilling and the inference of periphery metabolic pathways based on lower-confidence annotations. The central carbon pathways and electron transport chains are among the most well-understood regions of microbial metabolism, and these pathways contribute significantly toward defining cellular behavior and growth conditions. Thus, it is often useful to construct a simplified core metabolic model (CMM) that is comprised of only the high-confidence central pathways. In this chapter, we discuss methods for producing core metabolic models (CMM) based on genome annotations. With its reduced scope compared to GEMs, CMM reconstruction focuses on accurate representation of the central metabolic pathways related to energy biosynthesis and accurate energy yield predictions. We demonstrate the reconstruction and analysis of CMMs using the DOE Systems Biology Knowledgebase (KBase). The complete workflow is available at http://kbase.us/core-models/.
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Affiliation(s)
- Janaka N Edirisinghe
- Computation Institute, University of Chicago, Chicago, IL, USA.
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, USA.
| | - José P Faria
- Computation Institute, University of Chicago, Chicago, IL, USA
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, USA
| | - Nomi L Harris
- Environmental Genomics and Systems Biology Division, E. O. Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Benjamin H Allen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Christopher S Henry
- Computation Institute, University of Chicago, Chicago, IL, USA.
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, USA.
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24
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Isom GL, Davies NJ, Chong ZS, Bryant JA, Jamshad M, Sharif M, Cunningham AF, Knowles TJ, Chng SS, Cole JA, Henderson IR. MCE domain proteins: conserved inner membrane lipid-binding proteins required for outer membrane homeostasis. Sci Rep 2017; 7:8608. [PMID: 28819315 PMCID: PMC5561183 DOI: 10.1038/s41598-017-09111-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 07/20/2017] [Indexed: 01/12/2023] Open
Abstract
Bacterial proteins with MCE domains were first described as being important for Mammalian Cell Entry. More recent evidence suggests they are components of lipid ABC transporters. In Escherichia coli, the single-domain protein MlaD is known to be part of an inner membrane transporter that is important for maintenance of outer membrane lipid asymmetry. Here we describe two multi MCE domain-containing proteins in Escherichia coli, PqiB and YebT, the latter of which is an orthologue of MAM-7 that was previously reported to be an outer membrane protein. We show that all three MCE domain-containing proteins localise to the inner membrane. Bioinformatic analyses revealed that MCE domains are widely distributed across bacterial phyla but multi MCE domain-containing proteins evolved in Proteobacteria from single-domain proteins. Mutants defective in mlaD, pqiAB and yebST were shown to have distinct but partially overlapping phenotypes, but the primary functions of PqiB and YebT differ from MlaD. Complementing our previous findings that all three proteins bind phospholipids, results presented here indicate that multi-domain proteins evolved in Proteobacteria for specific functions in maintaining cell envelope homeostasis.
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Affiliation(s)
- Georgia L Isom
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Nathaniel J Davies
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, United Kingdom
| | - Zhi-Soon Chong
- Department of Chemistry, National University of Singapore, Singapore, Singapore
| | - Jack A Bryant
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Mohammed Jamshad
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Maria Sharif
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Adam F Cunningham
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Timothy J Knowles
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Shu-Sin Chng
- Department of Chemistry, National University of Singapore, Singapore, Singapore
| | - Jeffrey A Cole
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Ian R Henderson
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom.
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25
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Shahmuradov IA, Mohamad Razali R, Bougouffa S, Radovanovic A, Bajic VB. bTSSfinder: a novel tool for the prediction of promoters in cyanobacteria and Escherichia coli. Bioinformatics 2017; 33:334-340. [PMID: 27694198 PMCID: PMC5408793 DOI: 10.1093/bioinformatics/btw629] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 09/27/2016] [Indexed: 12/01/2022] Open
Abstract
Motivation The computational search for promoters in prokaryotes remains an attractive problem in bioinformatics. Despite the attention it has received for many years, the problem has not been addressed satisfactorily. In any bacterial genome, the transcription start site is chosen mostly by the sigma (σ) factor proteins, which control the gene activation. The majority of published bacterial promoter prediction tools target σ70 promoters in Escherichia coli. Moreover, no σ-specific classification of promoters is available for prokaryotes other than for E. coli. Results Here, we introduce bTSSfinder, a novel tool that predicts putative promoters for five classes of σ factors in Cyanobacteria (σA, σC, σH, σG and σF) and for five classes of sigma factors in E. coli (σ70, σ38, σ32, σ28 and σ24). Comparing to currently available tools, bTSSfinder achieves higher accuracy (MCC = 0.86, F1-score = 0.93) compared to the next best tool with MCC = 0.59, F1-score = 0.79) and covers multiple classes of promoters. Availability and Implementation bTSSfinder is available standalone and online at http://www.cbrc.kaust.edu.sa/btssfinder. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Ilham Ayub Shahmuradov
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), 4700 King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Rozaimi Mohamad Razali
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), 4700 King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Salim Bougouffa
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), 4700 King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Aleksandar Radovanovic
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), 4700 King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Vladimir B Bajic
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), 4700 King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
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26
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Jeong H, Sim YM, Kim HJ, Lee SJ. Unveiling the Hybrid Genome Structure of Escherichia coli RR1 (HB101 RecA +). Front Microbiol 2017; 8:585. [PMID: 28421066 PMCID: PMC5379014 DOI: 10.3389/fmicb.2017.00585] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Accepted: 03/21/2017] [Indexed: 01/26/2023] Open
Abstract
There have been extensive genome sequencing studies for Escherichia coli strains, particularly for pathogenic isolates, because fast determination of pathogenic potential and/or drug resistance and their propagation routes is crucial. For laboratory E. coli strains, however, genome sequence information is limited except for several well-known strains. We determined the complete genome sequence of laboratory E. coli strain RR1 (HB101 RecA+), which has long been used as a general cloning host. A hybrid genome sequence of K-12 MG1655 and B BL21(DE3) was constructed based on the initial mapping of Illumina HiSeq reads to each reference, and iterative rounds of read mapping, variant detection, and consensus extraction were carried out. Finally, PCR and Sanger sequencing-based finishing were applied to resolve non-single nucleotide variant regions with aberrant read depths and breakpoints, most of them resulting from prophages and insertion sequence transpositions that are not present in the reference genome sequence. We found that 96.9% of the RR1 genome is derived from K-12, and identified exact crossover junctions between K-12 and B genomic fragments. However, because RR1 has experienced a series of genetic manipulations since branching from the common ancestor, it has a set of mutations different from those found in K-12 MG1655. As well as identifying all known genotypes of RR1 on the basis of genomic context, we found novel mutations. Our results extend current knowledge of the genotype of RR1 and its relatives, and provide insights into the pedigree, genomic background, and physiology of common laboratory strains.
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Affiliation(s)
- Haeyoung Jeong
- Infectious Disease Research Center, Korea Research Institute of Bioscience and BiotechnologyDaejeon, South Korea.,Biosystems and Bioengineering Program, University of Science and TechnologyDaejeon, South Korea
| | - Young Mi Sim
- Korean Bioinformation Center, Korea Research Institute of Bioscience and BiotechnologyDaejeon, South Korea
| | - Hyun Ju Kim
- Biosystems and Bioengineering Program, University of Science and TechnologyDaejeon, South Korea
| | - Sang Jun Lee
- Department of Systems Biotechnology, Chung-Ang UniversityAnseong, South Korea
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27
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Saeki K, Tominaga M, Kawai-Noma S, Saito K, Umeno D. Rapid Diversification of BetI-Based Transcriptional Switches for the Control of Biosynthetic Pathways and Genetic Circuits. ACS Synth Biol 2016; 5:1201-1210. [PMID: 26991155 DOI: 10.1021/acssynbio.5b00230] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Synthetic biologists are in need of genetic switches, or inducible sensor/promoter systems, that can be reliably integrated in multiple contexts. Using a liquid-based selection method, we systematically engineered the choline-inducible transcription factor BetI, yielding various choline-inducible and choline-repressive promoter systems with various input-output characteristics. In addition to having high stringency and a high maximum induction level, they underwent a graded and single-peaked response to choline. Taking advantage of these features, we demonstrated the utility of these systems for controlling the carotenoid biosynthetic pathway and for constructing two-input logic gates. Additionally, we demonstrated the rapidity, throughput, robustness, and cost-effectiveness of our selection method, which facilitates the conversion of natural genetic controlling systems into systems that are designed for various synthetic biology applications.
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Affiliation(s)
- Kazuya Saeki
- Department
of Applied Chemistry and Biotechnology, Faculty of Engineering, Chiba University, 1-33 Yayoi-Cyo, Inage-ku, Chiba 263-8522, Japan
| | - Masahiro Tominaga
- Department
of Applied Chemistry and Biotechnology, Faculty of Engineering, Chiba University, 1-33 Yayoi-Cyo, Inage-ku, Chiba 263-8522, Japan
| | - Shigeko Kawai-Noma
- Department
of Applied Chemistry and Biotechnology, Faculty of Engineering, Chiba University, 1-33 Yayoi-Cyo, Inage-ku, Chiba 263-8522, Japan
| | - Kyoichi Saito
- Department
of Applied Chemistry and Biotechnology, Faculty of Engineering, Chiba University, 1-33 Yayoi-Cyo, Inage-ku, Chiba 263-8522, Japan
| | - Daisuke Umeno
- Department
of Applied Chemistry and Biotechnology, Faculty of Engineering, Chiba University, 1-33 Yayoi-Cyo, Inage-ku, Chiba 263-8522, Japan
- Precursory Research
for Embryonic Science and Technology (PRESTO), Japan Science and Technology
Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
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28
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Baa-Puyoulet P, Parisot N, Febvay G, Huerta-Cepas J, Vellozo AF, Gabaldón T, Calevro F, Charles H, Colella S. ArthropodaCyc: a CycADS powered collection of BioCyc databases to analyse and compare metabolism of arthropods. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2016; 2016:baw081. [PMID: 27242037 PMCID: PMC5630938 DOI: 10.1093/database/baw081] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 04/25/2016] [Indexed: 01/25/2023]
Abstract
Arthropods interact with humans at different levels with highly beneficial roles (e.g. as pollinators), as well as with a negative impact for example as vectors of human or animal diseases, or as agricultural pests. Several arthropod genomes are available at present and many others will be sequenced in the near future in the context of the i5K initiative, offering opportunities for reconstructing, modelling and comparing their metabolic networks. In-depth analysis of these genomic data through metabolism reconstruction is expected to contribute to a better understanding of the biology of arthropods, thereby allowing the development of new strategies to control harmful species. In this context, we present here ArthropodaCyc, a dedicated BioCyc collection of databases using the Cyc annotation database system (CycADS), allowing researchers to perform reliable metabolism comparisons of fully sequenced arthropods genomes. Since the annotation quality is a key factor when performing such global genome comparisons, all proteins from the genomes included in the ArthropodaCyc database were re-annotated using several annotation tools and orthology information. All functional/domain annotation results and their sources were integrated in the databases for user access. Currently, ArthropodaCyc offers a centralized repository of metabolic pathways, protein sequence domains, Gene Ontology annotations as well as evolutionary information for 28 arthropod species. Such database collection allows metabolism analysis both with integrated tools and through extraction of data in formats suitable for systems biology studies. Database URL:http://arthropodacyc.cycadsys.org/
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Affiliation(s)
| | - Nicolas Parisot
- Univ Lyon, INSA-Lyon, INRA, BF2I, UMR0203, F-69621, Villeurbanne, France
| | - Gérard Febvay
- Univ Lyon, INSA-Lyon, INRA, BF2I, UMR0203, F-69621, Villeurbanne, France
| | - Jaime Huerta-Cepas
- Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Augusto F Vellozo
- Univ Lyon, Univ Lyon1, CNRS, LBBE, UMR5558, F-69622, Villeurbanne, France
| | - Toni Gabaldón
- Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain
| | - Federica Calevro
- Univ Lyon, INSA-Lyon, INRA, BF2I, UMR0203, F-69621, Villeurbanne, France
| | - Hubert Charles
- Univ Lyon, INSA-Lyon, INRA, BF2I, UMR0203, F-69621, Villeurbanne, France
| | - Stefano Colella
- Univ Lyon, INSA-Lyon, INRA, BF2I, UMR0203, F-69621, Villeurbanne, France
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29
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Shatsky M, Dong M, Liu H, Yang LL, Choi M, Singer ME, Geller JT, Fisher SJ, Hall SC, Hazen TC, Brenner SE, Butland G, Jin J, Witkowska HE, Chandonia JM, Biggin MD. Quantitative Tagless Copurification: A Method to Validate and Identify Protein-Protein Interactions. Mol Cell Proteomics 2016; 15:2186-202. [PMID: 27099342 PMCID: PMC5083090 DOI: 10.1074/mcp.m115.057117] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Indexed: 01/18/2023] Open
Abstract
Identifying protein-protein interactions (PPIs) at an acceptable false discovery rate (FDR) is challenging. Previously we identified several hundred PPIs from affinity purification - mass spectrometry (AP-MS) data for the bacteria Escherichia coli and Desulfovibrio vulgaris. These two interactomes have lower FDRs than any of the nine interactomes proposed previously for bacteria and are more enriched in PPIs validated by other data than the nine earlier interactomes. To more thoroughly determine the accuracy of ours or other interactomes and to discover further PPIs de novo, here we present a quantitative tagless method that employs iTRAQ MS to measure the copurification of endogenous proteins through orthogonal chromatography steps. 5273 fractions from a four-step fractionation of a D. vulgaris protein extract were assayed, resulting in the detection of 1242 proteins. Protein partners from our D. vulgaris and E. coli AP-MS interactomes copurify as frequently as pairs belonging to three benchmark data sets of well-characterized PPIs. In contrast, the protein pairs from the nine other bacterial interactomes copurify two- to 20-fold less often. We also identify 200 high confidence D. vulgaris PPIs based on tagless copurification and colocalization in the genome. These PPIs are as strongly validated by other data as our AP-MS interactomes and overlap with our AP-MS interactome for D.vulgaris within 3% of expectation, once FDRs and false negative rates are taken into account. Finally, we reanalyzed data from two quantitative tagless screens of human cell extracts. We estimate that the novel PPIs reported in these studies have an FDR of at least 85% and find that less than 7% of the novel PPIs identified in each screen overlap. Our results establish that a quantitative tagless method can be used to validate and identify PPIs, but that such data must be analyzed carefully to minimize the FDR.
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Affiliation(s)
- Maxim Shatsky
- From the ‡Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Ming Dong
- §Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Haichuan Liu
- ¶OB/GYN Department, University of California San Francisco-Sandler-Moore Mass Spectrometry Core Facility, University of California, San Francisco, California 94143
| | - Lee Lisheng Yang
- ‖Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Megan Choi
- §Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Mary E Singer
- **Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Jil T Geller
- **Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Susan J Fisher
- ¶OB/GYN Department, University of California San Francisco-Sandler-Moore Mass Spectrometry Core Facility, University of California, San Francisco, California 94143
| | - Steven C Hall
- ¶OB/GYN Department, University of California San Francisco-Sandler-Moore Mass Spectrometry Core Facility, University of California, San Francisco, California 94143
| | - Terry C Hazen
- ‡‡Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee 37996; §§Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Steven E Brenner
- From the ‡Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720; ¶¶Department of Plant and Microbial Biology, University of California, Berkeley, California 94720
| | - Gareth Butland
- ‖‖Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Jian Jin
- ‖Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - H Ewa Witkowska
- ¶OB/GYN Department, University of California San Francisco-Sandler-Moore Mass Spectrometry Core Facility, University of California, San Francisco, California 94143
| | - John-Marc Chandonia
- From the ‡Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720;
| | - Mark D Biggin
- §Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720;
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30
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Cordero N, Maza F, Navea-Perez H, Aravena A, Marquez-Fontt B, Navarrete P, Figueroa G, González M, Latorre M, Reyes-Jara A. Different Transcriptional Responses from Slow and Fast Growth Rate Strains of Listeria monocytogenes Adapted to Low Temperature. Front Microbiol 2016; 7:229. [PMID: 26973610 PMCID: PMC4772535 DOI: 10.3389/fmicb.2016.00229] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 02/12/2016] [Indexed: 01/12/2023] Open
Abstract
Listeria monocytogenes has become one of the principal foodborne pathogens worldwide. The capacity of this bacterium to grow at low temperatures has opened an interesting field of study in terms of the identification and classification of new strains of L. monocytogenes with different growth capacities at low temperatures. We determined the growth rate at 8°C of 110 strains of L. monocytogenes isolated from different food matrices. We identified a group of slow and fast strains according to their growth rate at 8°C and performed a global transcriptomic assay in strains previously adapted to low temperature. We then identified shared and specific transcriptional mechanisms, metabolic and cellular processes of both groups; bacterial motility was the principal process capable of differentiating the adaptation capacity of L. monocytogenes strains with different ranges of tolerance to low temperatures. Strains belonging to the fast group were less motile, which may allow these strains to achieve a greater rate of proliferation at low temperature.
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Affiliation(s)
- Ninoska Cordero
- Laboratorio de Microbiología y Probióticos, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile Santiago, Chile
| | - Felipe Maza
- Laboratorio de Microbiología y Probióticos, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile Santiago, Chile
| | - Helen Navea-Perez
- Laboratorio de Microbiología y Probióticos, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile Santiago, Chile
| | - Andrés Aravena
- Department of Molecular Biology and Genetics, Istanbul University Istanbul, Turkey
| | - Bárbara Marquez-Fontt
- Laboratorio de Microbiología y Probióticos, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile Santiago, Chile
| | - Paola Navarrete
- Laboratorio de Microbiología y Probióticos, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile Santiago, Chile
| | - Guillermo Figueroa
- Laboratorio de Microbiología y Probióticos, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile Santiago, Chile
| | - Mauricio González
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de ChileSantiago, Chile; Center for Genome Regulation (Fondap 15090007), Universidad de ChileSantiago, Chile
| | - Mauricio Latorre
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de ChileSantiago, Chile; Center for Genome Regulation (Fondap 15090007), Universidad de ChileSantiago, Chile; Mathomics, Center for Mathematical Modeling, Universidad de ChileSantiago, Chile
| | - Angélica Reyes-Jara
- Laboratorio de Microbiología y Probióticos, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile Santiago, Chile
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Shatsky M, Allen S, Gold BL, Liu NL, Juba TR, Reveco SA, Elias DA, Prathapam R, He J, Yang W, Szakal ED, Liu H, Singer ME, Geller JT, Lam BR, Saini A, Trotter VV, Hall SC, Fisher SJ, Brenner SE, Chhabra SR, Hazen TC, Wall JD, Witkowska HE, Biggin MD, Chandonia JM, Butland G. Bacterial Interactomes: Interacting Protein Partners Share Similar Function and Are Validated in Independent Assays More Frequently Than Previously Reported. Mol Cell Proteomics 2016; 15:1539-55. [PMID: 26873250 DOI: 10.1074/mcp.m115.054692] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Indexed: 01/31/2023] Open
Abstract
Numerous affinity purification-mass spectrometry (AP-MS) and yeast two-hybrid screens have each defined thousands of pairwise protein-protein interactions (PPIs), most of which are between functionally unrelated proteins. The accuracy of these networks, however, is under debate. Here, we present an AP-MS survey of the bacterium Desulfovibrio vulgaris together with a critical reanalysis of nine published bacterial yeast two-hybrid and AP-MS screens. We have identified 459 high confidence PPIs from D. vulgaris and 391 from Escherichia coli Compared with the nine published interactomes, our two networks are smaller, are much less highly connected, and have significantly lower false discovery rates. In addition, our interactomes are much more enriched in protein pairs that are encoded in the same operon, have similar functions, and are reproducibly detected in other physical interaction assays than the pairs reported in prior studies. Our work establishes more stringent benchmarks for the properties of protein interactomes and suggests that bona fide PPIs much more frequently involve protein partners that are annotated with similar functions or that can be validated in independent assays than earlier studies suggested.
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Affiliation(s)
- Maxim Shatsky
- From the Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720
| | - Simon Allen
- the Department of Obstetrics, Gynecology and Reproductive Sciences and Sandler-Moore Mass Spectrometry Core Facility, University of California at San Francisco, San Francisco, California, 94143
| | - Barbara L Gold
- the Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720
| | - Nancy L Liu
- the Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720
| | - Thomas R Juba
- the Departments of Biochemistry and of Molecular Microbiology and Immunology, University of Missouri, Columbia, Missouri, 65211
| | - Sonia A Reveco
- From the Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720
| | - Dwayne A Elias
- the Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, 37831
| | - Ramadevi Prathapam
- the Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720
| | - Jennifer He
- the Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720
| | - Wenhong Yang
- the Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720
| | - Evelin D Szakal
- the Department of Obstetrics, Gynecology and Reproductive Sciences and Sandler-Moore Mass Spectrometry Core Facility, University of California at San Francisco, San Francisco, California, 94143
| | - Haichuan Liu
- the Department of Obstetrics, Gynecology and Reproductive Sciences and Sandler-Moore Mass Spectrometry Core Facility, University of California at San Francisco, San Francisco, California, 94143
| | - Mary E Singer
- the Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720
| | - Jil T Geller
- the Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720
| | - Bonita R Lam
- the Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720
| | - Avneesh Saini
- the Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720
| | - Valentine V Trotter
- the Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720
| | - Steven C Hall
- the Department of Obstetrics, Gynecology and Reproductive Sciences and Sandler-Moore Mass Spectrometry Core Facility, University of California at San Francisco, San Francisco, California, 94143
| | - Susan J Fisher
- the Department of Obstetrics, Gynecology and Reproductive Sciences and Sandler-Moore Mass Spectrometry Core Facility, University of California at San Francisco, San Francisco, California, 94143
| | - Steven E Brenner
- From the Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720; the Department of Plant and Microbial Biology, University of California at Berkeley, Berkeley, California, 94720
| | - Swapnil R Chhabra
- From the Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720
| | - Terry C Hazen
- the Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee, 37996; and
| | - Judy D Wall
- the Departments of Biochemistry and of Molecular Microbiology and Immunology, University of Missouri, Columbia, Missouri, 65211
| | - H Ewa Witkowska
- the Department of Obstetrics, Gynecology and Reproductive Sciences and Sandler-Moore Mass Spectrometry Core Facility, University of California at San Francisco, San Francisco, California, 94143
| | - Mark D Biggin
- the Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720
| | - John-Marc Chandonia
- From the Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720;
| | - Gareth Butland
- the Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720; From the Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720;
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Babnigg G, Jedrzejczak R, Nocek B, Stein A, Eschenfeldt W, Stols L, Marshall N, Weger A, Wu R, Donnelly M, Joachimiak A. Gene selection and cloning approaches for co-expression and production of recombinant protein-protein complexes. JOURNAL OF STRUCTURAL AND FUNCTIONAL GENOMICS 2015; 16:113-28. [PMID: 26671275 PMCID: PMC6886524 DOI: 10.1007/s10969-015-9200-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 11/27/2015] [Indexed: 10/22/2022]
Abstract
Multiprotein complexes play essential roles in all cells and X-ray crystallography can provide unparalleled insight into their structure and function. Many of these complexes are believed to be sufficiently stable for structural biology studies, but the production of protein-protein complexes using recombinant technologies is still labor-intensive. We have explored several strategies for the identification and cloning of heterodimers and heterotrimers that are compatible with the high-throughput (HTP) structural biology pipeline developed for single proteins. Two approaches are presented and compared which resulted in co-expression of paired genes from a single expression vector. Native operons encoding predicted interacting proteins were selected from a repertoire of genomes, and cloned directly to expression vector. In an alternative approach, Helicobacter pylori proteins predicted to interact strongly were cloned, each associated with translational control elements, then linked into an artificial operon. Proteins were then expressed and purified by standard HTP protocols, resulting to date in the structure determination of two H. pylori complexes.
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Affiliation(s)
- György Babnigg
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, 9700 S Cass Ave., Argonne, IL, 60439, USA.
| | - Robert Jedrzejczak
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, 9700 S Cass Ave., Argonne, IL, 60439, USA
| | - Boguslaw Nocek
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, 9700 S Cass Ave., Argonne, IL, 60439, USA
| | - Adam Stein
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, 9700 S Cass Ave., Argonne, IL, 60439, USA
| | - William Eschenfeldt
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, 9700 S Cass Ave., Argonne, IL, 60439, USA
| | - Lucy Stols
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, 9700 S Cass Ave., Argonne, IL, 60439, USA
| | - Norman Marshall
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, 9700 S Cass Ave., Argonne, IL, 60439, USA
| | - Alicia Weger
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, 9700 S Cass Ave., Argonne, IL, 60439, USA
| | - Ruiying Wu
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, 9700 S Cass Ave., Argonne, IL, 60439, USA
| | - Mark Donnelly
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, 9700 S Cass Ave., Argonne, IL, 60439, USA
| | - Andrzej Joachimiak
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, 9700 S Cass Ave., Argonne, IL, 60439, USA.
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33
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Mao X, Ma Q, Liu B, Chen X, Zhang H, Xu Y. Revisiting operons: an analysis of the landscape of transcriptional units in E. coli. BMC Bioinformatics 2015; 16:356. [PMID: 26538447 PMCID: PMC4634151 DOI: 10.1186/s12859-015-0805-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 10/29/2015] [Indexed: 11/21/2022] Open
Abstract
Background Bacterial operons are considerably more complex than what were thought. At least their components are dynamically rather than statically defined as previously assumed. Here we present a computational study of the landscape of the transcriptional units (TUs) of E. coli K12, revealed by the available genomic and transcriptomic data, providing new understanding about the complexity of TUs as a whole encoded in the genome of E. coli K12. Results and conclusion Our main findings include that (i) different TUs may overlap with each other by sharing common genes, giving rise to clusters of overlapped TUs (TUCs) along the genomic sequence; (ii) the intergenic regions in front of the first gene of each TU tend to have more conserved sequence motifs than those of the other genes inside the TU, suggesting that TUs each have their own promoters; (iii) the terminators associated with the 3’ ends of TUCs tend to be Rho-independent terminators, substantially more often than terminators of TUs that end inside a TUC; and (iv) the functional relatedness of adjacent gene pairs in individual TUs is higher than those in TUCs, suggesting that individual TUs are more basic functional units than TUCs. Electronic supplementary material The online version of this article (doi:10.1186/s12859-015-0805-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xizeng Mao
- Computational Systems Biology Lab, Department of Biochemistry and Molecular Biology, and Institute of Bioinformatics, University of Georgia, Athens, USA. .,Present address: MD Anderson Cancer Center, Houston, TX, 77054, USA.
| | - Qin Ma
- Computational Systems Biology Lab, Department of Biochemistry and Molecular Biology, and Institute of Bioinformatics, University of Georgia, Athens, USA. .,BioEnergy Research Center (BESC), Athens, GA, USA. .,Present address: Department of Plant Science, South Dakota State University, Brookings, SD, 57006, USA. .,Present address: BioSNTR, Brookings, SD, USA.
| | - Bingqiang Liu
- School of Mathematics, Shandong University, Jinan, Shandong, China.
| | - Xin Chen
- Computational Systems Biology Lab, Department of Biochemistry and Molecular Biology, and Institute of Bioinformatics, University of Georgia, Athens, USA. .,College of Computer Sciences and Technology, Changchun, Jilin, China.
| | - Hanyuan Zhang
- Computational Systems Biology Lab, Department of Biochemistry and Molecular Biology, and Institute of Bioinformatics, University of Georgia, Athens, USA. .,Present address: Systems Biology and Biomedical Informatics (SBBI) Laboratory University of Nebraska-Lincoln 122B/122C Avery Hall, 1144 T St, Lincoln, NE, 68588-0115, USA.
| | - Ying Xu
- Computational Systems Biology Lab, Department of Biochemistry and Molecular Biology, and Institute of Bioinformatics, University of Georgia, Athens, USA. .,BioEnergy Research Center (BESC), Athens, GA, USA. .,College of Computer Sciences and Technology, Changchun, Jilin, China. .,School of Public Health, Jilin University, Changchun, Jilin, China.
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Konwar KM, Hanson NW, Bhatia MP, Kim D, Wu SJ, Hahn AS, Morgan-Lang C, Cheung HK, Hallam SJ. MetaPathways v2.5: quantitative functional, taxonomic and usability improvements. Bioinformatics 2015; 31:3345-7. [PMID: 26076725 PMCID: PMC4595896 DOI: 10.1093/bioinformatics/btv361] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 06/05/2015] [Indexed: 11/23/2022] Open
Abstract
Summary: Next-generation sequencing is producing vast amounts of sequence information from natural and engineered ecosystems. Although this data deluge has an enormous potential to transform our lives, knowledge creation and translation need software applications that scale with increasing data processing and analysis requirements. Here, we present improvements to MetaPathways, an annotation and analysis pipeline for environmental sequence information that expedites this transformation. We specifically address pathway prediction hazards through integration of a weighted taxonomic distance and enable quantitative comparison of assembled annotations through a normalized read-mapping measure. Additionally, we improve LAST homology searches through BLAST-equivalent E-values and output formats that are natively compatible with prevailing software applications. Finally, an updated graphical user interface allows for keyword annotation query and projection onto user-defined functional gene hierarchies, including the Carbohydrate-Active Enzyme database. Availability and implementation: MetaPathways v2.5 is available on GitHub: http://github.com/hallamlab/metapathways2. Contact:shallam@mail.ubc.ca Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Kishori M Konwar
- Department of Microbiology & Immunology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, Canada
| | - Niels W Hanson
- Graduate Program in Bioinformatics, University of British Columbia, Genome Sciences Centre, 100-570 West 7th Avenue, Vancouver, BC, Canada and
| | - Maya P Bhatia
- Department of Microbiology & Immunology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, Canada
| | - Dongjae Kim
- Department of Computer Science, University of British Columbia, 2366 Main Mall, Vancouver, BC, Canada
| | - Shang-Ju Wu
- Department of Computer Science, University of British Columbia, 2366 Main Mall, Vancouver, BC, Canada
| | - Aria S Hahn
- Department of Microbiology & Immunology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, Canada
| | - Connor Morgan-Lang
- Graduate Program in Bioinformatics, University of British Columbia, Genome Sciences Centre, 100-570 West 7th Avenue, Vancouver, BC, Canada and
| | - Hiu Kan Cheung
- Department of Microbiology & Immunology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, Canada
| | - Steven J Hallam
- Department of Microbiology & Immunology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, Canada, Graduate Program in Bioinformatics, University of British Columbia, Genome Sciences Centre, 100-570 West 7th Avenue, Vancouver, BC, Canada and
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35
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Xie T, Fu LY, Yang QY, Xiong H, Xu H, Ma BG, Zhang HY. Spatial features for Escherichia coli genome organization. BMC Genomics 2015; 16:37. [PMID: 25652224 PMCID: PMC4326437 DOI: 10.1186/s12864-015-1258-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2014] [Accepted: 01/19/2015] [Indexed: 12/21/2022] Open
Abstract
Background In bacterial genomes, the compactly encoded genes and operons are well organized, with genes in the same biological pathway or operons in the same regulon close to each other on the genome sequence. In addition, the linearly close genes have a higher probability of co-expression and their protein products tend to form protein–protein interactions. However, the organization features of bacterial genomes in a three-dimensional space remain elusive. The DNA interaction data of Escherichia coli, measured by the genome conformation capture (GCC) technique, have recently become available, which allowed us to investigate the spatial features of bacterial genome organization. Results By renormalizing the GCC data, we compared the interaction frequency of operon pairs in the same regulon with that of random operon pairs. The results showed that arrangements of operons in the E. coli genome tend to minimize the spatial distance between operons in the same regulon. A similar global organization feature exists for genes in biological pathways of E. coli. In addition, the genes close to each other spatially (even if they are far from each other on the genome sequence) tend to be co-expressed and form protein–protein interactions. These results provided new insights into the organization principles of bacterial genomes and support the notion of transcription factory. Conclusions This study revealed the organization features of Escherichia coli genomic functional units in the 3D space and furthered our understanding of the link between the three-dimensional structure of chromosomes and biological function. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1258-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ting Xie
- National Key Laboratory of Crop Genetic Improvement, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, P. R. China.
| | - Liang-Yu Fu
- National Key Laboratory of Crop Genetic Improvement, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, P. R. China.
| | - Qing-Yong Yang
- National Key Laboratory of Crop Genetic Improvement, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, P. R. China.
| | - Heng Xiong
- National Key Laboratory of Crop Genetic Improvement, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, P. R. China.
| | - Hongrui Xu
- National Key Laboratory of Crop Genetic Improvement, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, P. R. China.
| | - Bin-Guang Ma
- National Key Laboratory of Crop Genetic Improvement, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, P. R. China.
| | - Hong-Yu Zhang
- National Key Laboratory of Crop Genetic Improvement, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, P. R. China.
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Abstract
With current advances in genomics, several technological processes have been generated, resulting in improvement in different segments of molecular research involving prokaryotic and eukaryotic systems. A widely used contribution is the identification of new genes and their functions, which has led to the elucidation of several issues concerning cell regulation and interactions. For this, increase in the knowledge generated from the identification of promoters becomes considerably relevant, especially considering that to generate new technological processes, such as genetically modified organisms, the availability of promoters that regulate the expression of new genes is still limited. Considering that this issue is essential for biotechnologists, this paper presents an updated review of promoters, from their structure to expression, and focuses on the knowledge already available in eukaryotic systems. Information on current promoters and methodologies available for studying their expression are also reported.
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37
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Gómez-Sagasti MT, Becerril JM, Martín I, Epelde L, Garbisu C. cDNA microarray assessment of early gene expression profiles in Escherichia coli cells exposed to a mixture of heavy metals. Cell Biol Toxicol 2014; 30:207-32. [DOI: 10.1007/s10565-014-9281-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Accepted: 06/12/2014] [Indexed: 12/30/2022]
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38
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Karp PD, Weaver D, Paley S, Fulcher C, Kubo A, Kothari A, Krummenacker M, Subhraveti P, Weerasinghe D, Gama-Castro S, Huerta AM, Muñiz-Rascado L, Bonavides-Martinez C, Weiss V, Peralta-Gil M, Santos-Zavaleta A, Schröder I, Mackie A, Gunsalus R, Collado-Vides J, Keseler IM, Paulsen I. The EcoCyc Database. EcoSal Plus 2014; 6:10.1128/ecosalplus.ESP-0009-2013. [PMID: 26442933 PMCID: PMC4243172 DOI: 10.1128/ecosalplus.esp-0009-2013] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Indexed: 11/20/2022]
Abstract
EcoCyc is a bioinformatics database available at EcoCyc.org that describes the genome and the biochemical machinery of Escherichia coli K-12 MG1655. The long-term goal of the project is to describe the complete molecular catalog of the E. coli cell, as well as the functions of each of its molecular parts, to facilitate a system-level understanding of E. coli. EcoCyc is an electronic reference source for E. coli biologists and for biologists who work with related microorganisms. The database includes information pages on each E. coli gene, metabolite, reaction, operon, and metabolic pathway. The database also includes information on E. coli gene essentiality and on nutrient conditions that do or do not support the growth of E. coli. The website and downloadable software contain tools for analysis of high-throughput data sets. In addition, a steady-state metabolic flux model is generated from each new version of EcoCyc. The model can predict metabolic flux rates, nutrient uptake rates, and growth rates for different gene knockouts and nutrient conditions. This review provides a detailed description of the data content of EcoCyc and of the procedures by which this content is generated.
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Affiliation(s)
- Peter D Karp
- Bioinformatics Research Group, SRI International, Menlo Park, CA 94025
| | - Daniel Weaver
- Bioinformatics Research Group, SRI International, Menlo Park, CA 94025
| | - Suzanne Paley
- Bioinformatics Research Group, SRI International, Menlo Park, CA 94025
| | - Carol Fulcher
- Bioinformatics Research Group, SRI International, Menlo Park, CA 94025
| | - Aya Kubo
- Bioinformatics Research Group, SRI International, Menlo Park, CA 94025
| | - Anamika Kothari
- Bioinformatics Research Group, SRI International, Menlo Park, CA 94025
| | | | | | | | - Socorro Gama-Castro
- Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, A.P. 565-A, Cuernavaca, Morelos 62100, México
| | - Araceli M Huerta
- Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, A.P. 565-A, Cuernavaca, Morelos 62100, México
| | - Luis Muñiz-Rascado
- Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, A.P. 565-A, Cuernavaca, Morelos 62100, México
| | - César Bonavides-Martinez
- Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, A.P. 565-A, Cuernavaca, Morelos 62100, México
| | - Verena Weiss
- Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, A.P. 565-A, Cuernavaca, Morelos 62100, México
| | - Martin Peralta-Gil
- Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, A.P. 565-A, Cuernavaca, Morelos 62100, México
| | - Alberto Santos-Zavaleta
- Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, A.P. 565-A, Cuernavaca, Morelos 62100, México
| | - Imke Schröder
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA 90095
- UCLA Institute of Genomics and Proteomics, University of California, Los Angeles, CA 90095
| | - Amanda Mackie
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Robert Gunsalus
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA 90095
| | - Julio Collado-Vides
- Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, A.P. 565-A, Cuernavaca, Morelos 62100, México
| | - Ingrid M Keseler
- Bioinformatics Research Group, SRI International, Menlo Park, CA 94025
| | - Ian Paulsen
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
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Investigating host-pathogen behavior and their interaction using genome-scale metabolic network models. Methods Mol Biol 2014; 1184:523-62. [PMID: 25048144 DOI: 10.1007/978-1-4939-1115-8_29] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Genome Scale Metabolic Modeling methods represent one way to compute whole cell function starting from the genome sequence of an organism and contribute towards understanding and predicting the genotype-phenotype relationship. About 80 models spanning all the kingdoms of life from archaea to eukaryotes have been built till date and used to interrogate cell phenotype under varying conditions. These models have been used to not only understand the flux distribution in evolutionary conserved pathways like glycolysis and the Krebs cycle but also in applications ranging from value added product formation in Escherichia coli to predicting inborn errors of Homo sapiens metabolism. This chapter describes a protocol that delineates the process of genome scale metabolic modeling for analysing host-pathogen behavior and interaction using flux balance analysis (FBA). The steps discussed in the process include (1) reconstruction of a metabolic network from the genome sequence, (2) its representation in a precise mathematical framework, (3) its translation to a model, and (4) the analysis using linear algebra and optimization. The methods for biological interpretations of computed cell phenotypes in the context of individual host and pathogen models and their integration are also discussed.
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Yang Y, Maxwell A, Zhang X, Wang N, Perkins EJ, Zhang C, Gong P. Differential reconstructed gene interaction networks for deriving toxicity threshold in chemical risk assessment. BMC Bioinformatics 2013; 14 Suppl 14:S3. [PMID: 24268022 PMCID: PMC3851258 DOI: 10.1186/1471-2105-14-s14-s3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Background Pathway alterations reflected as changes in gene expression regulation and gene interaction can result from cellular exposure to toxicants. Such information is often used to elucidate toxicological modes of action. From a risk assessment perspective, alterations in biological pathways are a rich resource for setting toxicant thresholds, which may be more sensitive and mechanism-informed than traditional toxicity endpoints. Here we developed a novel differential networks (DNs) approach to connect pathway perturbation with toxicity threshold setting. Methods Our DNs approach consists of 6 steps: time-series gene expression data collection, identification of altered genes, gene interaction network reconstruction, differential edge inference, mapping of genes with differential edges to pathways, and establishment of causal relationships between chemical concentration and perturbed pathways. A one-sample Gaussian process model and a linear regression model were used to identify genes that exhibited significant profile changes across an entire time course and between treatments, respectively. Interaction networks of differentially expressed (DE) genes were reconstructed for different treatments using a state space model and then compared to infer differential edges/interactions. DE genes possessing differential edges were mapped to biological pathways in databases such as KEGG pathways. Results Using the DNs approach, we analyzed a time-series Escherichia coli live cell gene expression dataset consisting of 4 treatments (control, 10, 100, 1000 mg/L naphthenic acids, NAs) and 18 time points. Through comparison of reconstructed networks and construction of differential networks, 80 genes were identified as DE genes with a significant number of differential edges, and 22 KEGG pathways were altered in a concentration-dependent manner. Some of these pathways were perturbed to a degree as high as 70% even at the lowest exposure concentration, implying a high sensitivity of our DNs approach. Conclusions Findings from this proof-of-concept study suggest that our approach has a great potential in providing a novel and sensitive tool for threshold setting in chemical risk assessment. In future work, we plan to analyze more time-series datasets with a full spectrum of concentrations and sufficient replications per treatment. The pathway alteration-derived thresholds will also be compared with those derived from apical endpoints such as cell growth rate.
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Li S, Dong X, Su Z. Directional RNA-seq reveals highly complex condition-dependent transcriptomes in E. coli K12 through accurate full-length transcripts assembling. BMC Genomics 2013; 14:520. [PMID: 23899370 PMCID: PMC3734233 DOI: 10.1186/1471-2164-14-520] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Accepted: 07/27/2013] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Although prokaryotic gene transcription has been studied over decades, many aspects of the process remain poorly understood. Particularly, recent studies have revealed that transcriptomes in many prokaryotes are far more complex than previously thought. Genes in an operon are often alternatively and dynamically transcribed under different conditions, and a large portion of genes and intergenic regions have antisense RNA (asRNA) and non-coding RNA (ncRNA) transcripts, respectively. Ironically, similar studies have not been conducted in the model bacterium E coli K12, thus it is unknown whether or not the bacterium possesses similar complex transcriptomes. Furthermore, although RNA-seq becomes the major method for analyzing the complexity of prokaryotic transcriptome, it is still a challenging task to accurately assemble full length transcripts using short RNA-seq reads. RESULTS To fill these gaps, we have profiled the transcriptomes of E. coli K12 under different culture conditions and growth phases using a highly specific directional RNA-seq technique that can capture various types of transcripts in the bacterial cells, combined with a highly accurate and robust algorithm and tool TruHMM (http://bioinfolab.uncc.edu/TruHmm_package/) for assembling full length transcripts. We found that 46.9 ~ 63.4% of expressed operons were utilized in their putative alternative forms, 72.23 ~ 89.54% genes had putative asRNA transcripts and 51.37 ~ 72.74% intergenic regions had putative ncRNA transcripts under different culture conditions and growth phases. CONCLUSIONS As has been demonstrated in many other prokaryotes, E. coli K12 also has a highly complex and dynamic transcriptomes under different culture conditions and growth phases. Such complex and dynamic transcriptomes might play important roles in the physiology of the bacterium. TruHMM is a highly accurate and robust algorithm for assembling full-length transcripts in prokaryotes using directional RNA-seq short reads.
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Affiliation(s)
- Shan Li
- Department of Bioinformatics and Genomics, College of Computing and Informatics, The University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC 28223, USA
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Fang G, Passalacqua KD, Hocking J, Llopis PM, Gerstein M, Bergman NH, Jacobs-Wagner C. Transcriptomic and phylogenetic analysis of a bacterial cell cycle reveals strong associations between gene co-expression and evolution. BMC Genomics 2013; 14:450. [PMID: 23829427 PMCID: PMC3829707 DOI: 10.1186/1471-2164-14-450] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2012] [Accepted: 05/13/2013] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND The genetic network involved in the bacterial cell cycle is poorly understood even though it underpins the remarkable ability of bacteria to proliferate. How such network evolves is even less clear. The major aims of this work were to identify and examine the genes and pathways that are differentially expressed during the Caulobacter crescentus cell cycle, and to analyze the evolutionary features of the cell cycle network. RESULTS We used deep RNA sequencing to obtain high coverage RNA-Seq data of five C. crescentus cell cycle stages, each with three biological replicates. We found that 1,586 genes (over a third of the genome) display significant differential expression between stages. This gene list, which contains many genes previously unknown for their cell cycle regulation, includes almost half of the genes involved in primary metabolism, suggesting that these "house-keeping" genes are not constitutively transcribed during the cell cycle, as often assumed. Gene and module co-expression clustering reveal co-regulated pathways and suggest functionally coupled genes. In addition, an evolutionary analysis of the cell cycle network shows a high correlation between co-expression and co-evolution. Most co-expression modules have strong phylogenetic signals, with broadly conserved genes and clade-specific genes predominating different substructures of the cell cycle co-expression network. We also found that conserved genes tend to determine the expression profile of their module. CONCLUSION We describe the first phylogenetic and single-nucleotide-resolution transcriptomic analysis of a bacterial cell cycle network. In addition, the study suggests how evolution has shaped this network and provides direct biological network support that selective pressure is not on individual genes but rather on the relationship between genes, which highlights the importance of integrating phylogenetic analysis into biological network studies.
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Affiliation(s)
- Gang Fang
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA.
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Ma Q, Yin Y, Schell MA, Zhang H, Li G, Xu Y. Computational analyses of transcriptomic data reveal the dynamic organization of the Escherichia coli chromosome under different conditions. Nucleic Acids Res 2013; 41:5594-603. [PMID: 23599001 PMCID: PMC3675479 DOI: 10.1093/nar/gkt261] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The circular chromosome of Escherichia coli has been suggested to fold into a collection of sequentially consecutive domains, genes in each of which tend to be co-expressed. It has also been suggested that such domains, forming a partition of the genome, are dynamic with respect to the physiological conditions. However, little is known about which DNA segments of the E. coli genome form these domains and what determines the boundaries of these domain segments. We present a computational model here to partition the circular genome into consecutive segments, theoretically suggestive of the physically folded supercoiled domains, along with a method for predicting such domains under specified conditions. Our model is based on a hypothesis that the genome of E. coli is partitioned into a set of folding domains so that the total number of unfoldings of these domains in the folded chromosome is minimized, where a domain is unfolded when a biological pathway, consisting of genes encoded in this DNA segment, is being activated transcriptionally. Based on this hypothesis, we have predicted seven distinct sets of such domains along the E. coli genome for seven physiological conditions, namely exponential growth, stationary growth, anaerobiosis, heat shock, oxidative stress, nitrogen limitation and SOS responses. These predicted folding domains are highly stable statistically and are generally consistent with the experimental data of DNA binding sites of the nucleoid-associated proteins that assist the folding of these domains, as well as genome-scale protein occupancy profiles, hence supporting our proposed model. Our study established for the first time a strong link between a folded E. coli chromosomal structure and the encoded biological pathways and their activation frequencies.
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Affiliation(s)
- Qin Ma
- Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology and Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
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Remli MA, Deris S. An Approach for Biological Data Integration and Knowledge Retrieval Based on Ontology, Semantic Web Services Composition, and AI Planning. Bioinformatics 2013. [DOI: 10.4018/978-1-4666-3604-0.ch091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
This chapter describes an approach involved in two knowledge management processes in biological fields, namely data integration and knowledge retrieval based on ontology, Web services, and Artificial Intelligence (AI) planning. For the data integration, Semantic Web combining with ontology is promising several ways to integrate a heterogeneous biological database. The goal of this work is to construct an integration approach for gram-positive bacteria organism that combines gene, protein, and pathway, thus allowing biological questions to be answered. The authors present a new perspective to retrieve knowledge by using Semantic Web services composition and Artificial Intelligence (AI) planning system, Simple Hierarchical Order Planner 2 (SHOP2). A Semantic Web service annotated with domain ontology is used to describe services for biological pathway knowledge retrieval at Kyoto Encyclopedia of Gene and Genomes (KEGG) database. The authors investigate the effectiveness of this approach by applying a real world scenario in pathway information retrieval for an organism where the biologist needs to discover the pathway description from a given specific gene of interest. Both of these two processes (data integration and knowledge retrieval) used ontology as the key role to achieve the biological goals.
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Ma Q, Xu Y. Global genomic arrangement of bacterial genes is closely tied with the total transcriptional efficiency. GENOMICS PROTEOMICS & BIOINFORMATICS 2013; 11:66-71. [PMID: 23434046 PMCID: PMC4357662 DOI: 10.1016/j.gpb.2013.01.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Revised: 01/09/2013] [Accepted: 01/14/2013] [Indexed: 01/03/2023]
Abstract
The availability of a large number of sequenced bacterial genomes allows researchers not only to derive functional and regulation information about specific organisms but also to study the fundamental properties of the organization of a genome. Here we address an important and challenging question regarding the global arrangement of operons in a bacterial genome: why operons in a bacterial genome are arranged in the way they are. We have previously studied this question and found that operons of more frequently activated pathways tend to be more clustered together in a genome. Specifically, we have developed a simple sequential distance-based pseudo energy function and found that the arrangement of operons in a bacterial genome tend to minimize the clusteredness function (C value) in comparison with artificially-generated alternatives, for a variety of bacterial genomes. Here we extend our previous work, and report a number of new observations: (a) operons of the same pathways tend to group into a few clusters rather than one; and (b) the global arrangement of these operon clusters tend to minimize a new “energy” function (C+ value) that reflects the efficiency of the transcriptional activation of the encoded pathways. These observations provide insights into further study of the genomic organization of genes in bacteria.
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Affiliation(s)
- Qin Ma
- Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology and Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
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Walian PJ, Allen S, Shatsky M, Zeng L, Szakal ED, Liu H, Hall SC, Fisher SJ, Lam BR, Singer ME, Geller JT, Brenner SE, Chandonia JM, Hazen TC, Witkowska HE, Biggin MD, Jap BK. High-throughput isolation and characterization of untagged membrane protein complexes: outer membrane complexes of Desulfovibrio vulgaris. J Proteome Res 2012; 11:5720-35. [PMID: 23098413 PMCID: PMC3516867 DOI: 10.1021/pr300548d] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Cell membranes represent the “front line”
of cellular defense and the interface between a cell and its environment.
To determine the range of proteins and protein complexes that are
present in the cell membranes of a target organism, we have utilized
a “tagless” process for the system-wide isolation and
identification of native membrane protein complexes. As an initial
subject for study, we have chosen the Gram-negative sulfate-reducing
bacterium Desulfovibrio vulgaris. With this tagless
methodology, we have identified about two-thirds of the outer membrane-
associated proteins anticipated. Approximately three-fourths of these
appear to form homomeric complexes. Statistical and machine-learning
methods used to analyze data compiled over multiple experiments revealed
networks of additional protein–protein interactions providing
insight into heteromeric contacts made between proteins across this
region of the cell. Taken together, these results establish a D. vulgaris outer membrane protein data set that will be
essential for the detection and characterization of environment-driven
changes in the outer membrane proteome and in the modeling of stress
response pathways. The workflow utilized here should be effective
for the global characterization of membrane protein complexes in a
wide range of organisms.
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Affiliation(s)
- Peter J Walian
- Lawrence Berkeley National Laboratory, Berkeley, California, United States.
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Leiby N, Harcombe WR, Marx CJ. Multiple long-term, experimentally-evolved populations of Escherichia coli acquire dependence upon citrate as an iron chelator for optimal growth on glucose. BMC Evol Biol 2012; 12:151. [PMID: 22909317 PMCID: PMC3496695 DOI: 10.1186/1471-2148-12-151] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2012] [Accepted: 08/15/2012] [Indexed: 11/16/2022] Open
Abstract
Background Specialization for ecological niches is a balance of evolutionary adaptation and its accompanying tradeoffs. Here we focus on the Lenski Long-Term Evolution Experiment, which has maintained cultures of Escherichia coli in the same defined seasonal environment for 50,000 generations. Over this time, much adaptation and specialization to the environment has occurred. The presence of citrate in the growth media selected one lineage to gain the novel ability to utilize citrate as a carbon source after 31,000 generations. Here we test whether other strains have specialized to rely on citrate after 50,000 generations. Results We show that in addition to the citrate-catabolizing strain, three other lineages evolving in parallel have acquired a dependence on citrate for optimal growth on glucose. None of these strains were stimulated indirectly by the sodium present in disodium citrate, nor exhibited even partial utilization of citrate as a carbon source. Instead, all three of these citrate-stimulated populations appear to rely on it as a chelator of iron. Conclusions The strains we examine here have evolved specialization to their environment through apparent loss of function. Our results are most consistent with the accumulation of mutations in iron transport genes that were obviated by abundant citrate. The results present another example where a subtle decision in the design of an evolution experiment led to unexpected evolutionary outcomes.
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Affiliation(s)
- Nicholas Leiby
- 1Systems Biology Graduate Program, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
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Recombinant E. coli expressing Vitreoscilla haemoglobin prefers aerobic metabolism under microaerobic conditions: A proteome-level study. J Biosci 2012; 37:617-33. [DOI: 10.1007/s12038-012-9245-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Sasson V, Shachrai I, Bren A, Dekel E, Alon U. Mode of regulation and the insulation of bacterial gene expression. Mol Cell 2012; 46:399-407. [PMID: 22633488 DOI: 10.1016/j.molcel.2012.04.032] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2011] [Revised: 04/16/2012] [Accepted: 04/27/2012] [Indexed: 10/28/2022]
Abstract
A gene can be said to be insulated from environmental variations if its expression level depends only on its cognate inducers, and not on variations in conditions. We tested the insulation of the lac promoter of E. coli and of synthetic constructs in which the transcription factor CRP acts as either an activator or a repressor, by measuring their input function-their expression as a function of inducers-in different growth conditions. We find that the promoter activities show sizable variation across conditions of 10%-100% (SD/mean). When the promoter is bound to its cognate regulator(s), variation across conditions is smaller than when it is unbound. Thus, mode of regulation affects insulation: activators seem to show better insulation at high expression levels, and repressors at low expression levels. This may explain the Savageau demand rule, in which E. coli genes needed often in the natural environment tend to be regulated by activators, and rarely needed genes by repressors. The present approach can be used to study insulation in other genes and organisms.
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Affiliation(s)
- Vered Sasson
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
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Wang J, Zhang Y, Marian C, Ressom HW. Identification of aberrant pathways and network activities from high-throughput data. Brief Bioinform 2012; 13:406-19. [PMID: 22287794 PMCID: PMC3404398 DOI: 10.1093/bib/bbs001] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Revised: 01/03/2012] [Indexed: 02/06/2023] Open
Abstract
Many complex diseases such as cancer are associated with changes in biological pathways and molecular networks rather than being caused by single gene alterations. A major challenge in the diagnosis and treatment of such diseases is to identify characteristic aberrancies in the biological pathways and molecular network activities and elucidate their relationship to the disease. This review presents recent progress in using high-throughput biological assays to decipher aberrant pathways and network activities. In particular, this review provides specific examples in which high-throughput data have been applied to identify relationships between diseases and aberrant pathways and network activities. The achievements in this field have been remarkable, but many challenges have yet to be addressed.
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