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Popova L, Carr RA, Carabetta VJ. Recent Contributions of Proteomics to Our Understanding of Reversible N ε-Lysine Acylation in Bacteria. J Proteome Res 2024; 23:2733-2749. [PMID: 38442041 PMCID: PMC11296938 DOI: 10.1021/acs.jproteome.3c00912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2024]
Abstract
Post-translational modifications (PTMs) have been extensively studied in both eukaryotes and prokaryotes. Lysine acetylation, originally thought to be a rare occurrence in bacteria, is now recognized as a prevalent and important PTM in more than 50 species. This expansion in interest in bacterial PTMs became possible with the advancement of mass spectrometry technology and improved reagents such as acyl-modification specific antibodies. In this Review, we discuss how mass spectrometry-based proteomic studies of lysine acetylation and other acyl modifications have contributed to our understanding of bacterial physiology, focusing on recently published studies from 2018 to 2023. We begin with a discussion of approaches used to study bacterial PTMs. Next, we discuss newly characterized acylomes, including acetylomes, succinylomes, and malonylomes, in different bacterial species. In addition, we examine proteomic contributions to our understanding of bacterial virulence and biofilm formation. Finally, we discuss the contributions of mass spectrometry to our understanding of the mechanisms of acetylation, both enzymatic and nonenzymatic. We end with a discussion of the current state of the field and possible future research avenues to explore.
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Affiliation(s)
- Liya Popova
- Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden, New Jersey 08103, United States
| | - Rachel A Carr
- Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden, New Jersey 08103, United States
| | - Valerie J Carabetta
- Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden, New Jersey 08103, United States
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2
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Zhou H, Wang ZY, Li C, Yuan HW, Hu L, Zeng P, Yang WT, Liao BH, Gu JF. Straw removal reduces Cd availability and rice Cd accumulation in Cd-contaminated paddy soil: Cd fraction, soil microorganism structure and porewater DOC and Cd. JOURNAL OF HAZARDOUS MATERIALS 2024; 476:135189. [PMID: 39013317 DOI: 10.1016/j.jhazmat.2024.135189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Revised: 07/08/2024] [Accepted: 07/11/2024] [Indexed: 07/18/2024]
Abstract
The impacts of straw removal on rice Cd absorption, behaviour of Cd and microbial community in rhizosphere soil were investigated in paddy fields over two consecutive seasons. The results of the experiments in two fields revealed that straw removal promoted the transformation of soil Cd from acid-extractable and oxidisable fraction to residual fraction and reduced soil DTPA-Cd content with the reduction in DOC and Cd ions in soil porewater, thereby decreasing Cd content in rice. Specifically, the Cd content in brown rice of early rice was below 0.2 mg·kg-1 when all rice straw and roots were removed in the slightly Cd-contaminated soils. The α-diversity of soil microbial communities was less influenced by continuous straw removal, β-diversity was altered and the relative abundances of Anaeromyxobacter, Methylocystis and Mycobacterium microbes were increased. Redundancy analysis and network analysis exhibited that soil pH predominantly influenced the microbial community. Path analysis revealed that the Cd content in brown rice could be directly influenced by the soil Total-Cd and DTPA-Cd, as well as soil pH and OM. Straw removal, including roots removal, is an economical and effective technique to reduce Cd accumulation in rice plants.
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Affiliation(s)
- Hang Zhou
- College of Life and Environment Sciences, Central South University of Forestry and Technology, Changsha 410004, China; Hunan Provincial Soil Pollution Remediation and Carbon Fixation Engineering Technology Research Center, Changsha 410004, China; Yuelushan Laboratory, Changsha 410000, China.
| | - Zi-Yu Wang
- College of Life and Environment Sciences, Central South University of Forestry and Technology, Changsha 410004, China.
| | - Chang Li
- College of Life and Environment Sciences, Central South University of Forestry and Technology, Changsha 410004, China.
| | - Hai-Wei Yuan
- Hunan Provincial Soil Pollution Remediation and Carbon Fixation Engineering Technology Research Center, Changsha 410004, China; Hunan Huanbaoqiao Ecology and Environment Engineering Co., Ltd., Changsha 410205, China.
| | - Lu Hu
- Hunan Provincial Soil Pollution Remediation and Carbon Fixation Engineering Technology Research Center, Changsha 410004, China; Hunan Huanbaoqiao Ecology and Environment Engineering Co., Ltd., Changsha 410205, China.
| | - Peng Zeng
- College of Life and Environment Sciences, Central South University of Forestry and Technology, Changsha 410004, China; Hunan Provincial Soil Pollution Remediation and Carbon Fixation Engineering Technology Research Center, Changsha 410004, China; Yuelushan Laboratory, Changsha 410000, China.
| | - Wen-Tao Yang
- College of Resource and Environmental Engineering, Guizhou University, Guiyang 550025, China.
| | - Bo-Han Liao
- College of Life and Environment Sciences, Central South University of Forestry and Technology, Changsha 410004, China.
| | - Jiao-Feng Gu
- College of Life and Environment Sciences, Central South University of Forestry and Technology, Changsha 410004, China; Hunan Provincial Soil Pollution Remediation and Carbon Fixation Engineering Technology Research Center, Changsha 410004, China; Hunan Huanbaoqiao Ecology and Environment Engineering Co., Ltd., Changsha 410205, China; Yuelushan Laboratory, Changsha 410000, China.
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Lozano-Terol G, Chiozzi RZ, Gallego-Jara J, Sola-Martínez RA, Vivancos AM, Ortega Á, Heck AJ, Díaz MC, de Diego Puente T. Relative impact of three growth conditions on the Escherichia coli protein acetylome. iScience 2024; 27:109017. [PMID: 38333705 PMCID: PMC10850759 DOI: 10.1016/j.isci.2024.109017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 12/04/2023] [Accepted: 01/22/2024] [Indexed: 02/10/2024] Open
Abstract
Nε-lysine acetylation is a common posttranslational modification observed in Escherichia coli. In the present study, integrative analysis of the proteome and acetylome was performed using label-free quantitative mass spectrometry to analyze the relative influence of three factors affecting growth. The results revealed differences in the proteome, mainly owing to the type of culture medium used (defined or complex). In the acetylome, 7482 unique acetylation sites were identified. Acetylation is directly related to the abundance of proteins, and the level of acetylation in each type of culture is associated with extracellular acetate concentration. Furthermore, most acetylated lysines in the exponential phase remained in the stationary phase without dynamic turnover. Interestingly, unique acetylation sites were detected in proteins whose presence or abundance was linked to the type of culture medium. Finally, the biological function of the acetylation changes was demonstrated for three central metabolic proteins (GapA, Mdh, and AceA).
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Affiliation(s)
- Gema Lozano-Terol
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence “Campus Mare Nostrum”, 30100 Murcia, Spain
| | - Riccardo Zenezini Chiozzi
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padulaan 8, Utrecht 3584 CH, the Netherlands
| | - Julia Gallego-Jara
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence “Campus Mare Nostrum”, 30100 Murcia, Spain
| | - Rosa Alba Sola-Martínez
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence “Campus Mare Nostrum”, 30100 Murcia, Spain
| | - Adrián Martínez Vivancos
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence “Campus Mare Nostrum”, 30100 Murcia, Spain
| | - Álvaro Ortega
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence “Campus Mare Nostrum”, 30100 Murcia, Spain
| | - Albert J.R. Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padulaan 8, Utrecht 3584 CH, the Netherlands
| | - Manuel Cánovas Díaz
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence “Campus Mare Nostrum”, 30100 Murcia, Spain
| | - Teresa de Diego Puente
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence “Campus Mare Nostrum”, 30100 Murcia, Spain
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Longin H, Broeckaert N, Langen M, Hari R, Kramarska A, Oikarinen K, Hendrix H, Lavigne R, van Noort V. FLAMS: Find Lysine Acylations and other Modification Sites. Bioinformatics 2024; 40:btae005. [PMID: 38195744 PMCID: PMC10783949 DOI: 10.1093/bioinformatics/btae005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 12/04/2023] [Accepted: 01/08/2024] [Indexed: 01/11/2024] Open
Abstract
SUMMARY Today, hundreds of post-translational modification (PTM) sites are routinely identified at once, but the comparison of new experimental datasets to already existing ones is hampered by the current inability to search most PTM databases at the protein residue level. We present FLAMS (Find Lysine Acylations and other Modification Sites), a Python3-based command line and web-tool that enables researchers to compare their PTM sites to the contents of the CPLM, the largest dedicated protein lysine modification database, and dbPTM, the most comprehensive general PTM database, at the residue level. FLAMS can be integrated into PTM analysis pipelines, allowing researchers to quickly assess the novelty and conservation of PTM sites across species in newly generated datasets, aiding in the functional assessment of sites and the prioritization of sites for further experimental characterization. AVAILABILITY AND IMPLEMENTATION FLAMS is implemented in Python3, and freely available under an MIT license. It can be found as a command line tool at https://github.com/hannelorelongin/FLAMS, pip and conda; and as a web service at https://www.biw.kuleuven.be/m2s/cmpg/research/CSB/tools/flams/.
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Affiliation(s)
- Hannelore Longin
- KU Leuven, Department of Microbial and Molecular Systems, Computational Systems Biology, Leuven 3001, Belgium
- KU Leuven, Department of Biosystems, Laboratory of Gene Technology, Leuven 3001, Belgium
| | - Nand Broeckaert
- KU Leuven, Department of Microbial and Molecular Systems, Computational Systems Biology, Leuven 3001, Belgium
- KU Leuven, Department of Biosystems, Laboratory of Gene Technology, Leuven 3001, Belgium
| | - Maarten Langen
- KU Leuven, Department of Microbial and Molecular Systems, Computational Systems Biology, Leuven 3001, Belgium
| | - Roshan Hari
- KU Leuven, Department of Microbial and Molecular Systems, Computational Systems Biology, Leuven 3001, Belgium
| | - Anna Kramarska
- KU Leuven, Department of Microbial and Molecular Systems, Computational Systems Biology, Leuven 3001, Belgium
| | - Kasper Oikarinen
- KU Leuven, Department of Microbial and Molecular Systems, Computational Systems Biology, Leuven 3001, Belgium
| | - Hanne Hendrix
- KU Leuven, Department of Biosystems, Laboratory of Gene Technology, Leuven 3001, Belgium
| | - Rob Lavigne
- KU Leuven, Department of Biosystems, Laboratory of Gene Technology, Leuven 3001, Belgium
| | - Vera van Noort
- KU Leuven, Department of Microbial and Molecular Systems, Computational Systems Biology, Leuven 3001, Belgium
- Leiden University, Institute of Biology Leiden (IBL), Leiden 2333 BE, The Netherlands
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Dang H, Ewald JM, Mattes TE. Genome-Resolved Metagenomics and Metatranscriptomics Reveal Insights into the Ecology and Metabolism of Anaerobic Microbial Communities in PCB-Contaminated Sediments. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:16386-16398. [PMID: 37856784 PMCID: PMC10621002 DOI: 10.1021/acs.est.3c05439] [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: 07/10/2023] [Revised: 10/02/2023] [Accepted: 10/02/2023] [Indexed: 10/21/2023]
Abstract
Growth of organohalide-respiring bacteria such as Dehalococcoides mccartyi on halogenated organics (e.g., polychlorinated biphenyls (PCBs)) at contaminated sites or in enrichment culture requires interaction and support from other microbial community members. To evaluate naturally occurring interactions between Dehalococcoides and key supporting microorganisms (e.g., production of H2, acetate, and corrinoids) in PCB-contaminated sediments, metagenomic and metatranscriptomic sequencing was conducted on DNA and RNA extracted from sediment microcosms, showing evidence of both Dehalococcoides growth and PCB dechlorination. Using a genome-resolved approach, 160 metagenome-assembled genomes (MAGs), including three Dehalococcoides MAGs, were recovered. A novel reductive dehalogenase gene, distantly related to the chlorophenol dehalogenase gene cprA (pairwise amino acid identity: 23.75%), was significantly expressed. Using MAG gene expression data, 112 MAGs were assigned functional roles (e.g., corrinoid producers, acetate/H2 producers, etc.). A network coexpression analysis of all 160 MAGs revealed correlations between 39 MAGs and the Dehalococcoides MAGs. The network analysis also showed that MAGs assigned with functional roles that support Dehalococcoides growth (e.g., corrinoid assembly, and production of intermediates required for corrinoid synthesis) displayed significant coexpression correlations with Dehalococcoides MAGs. This work demonstrates the power of genome-resolved metagenomic and metatranscriptomic analyses, which unify taxonomy and function, in investigating the ecology of dehalogenating microbial communities.
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Affiliation(s)
- Hongyu Dang
- Department of Civil and Environmental
Engineering, 4105 Seamans Center, University
of Iowa, Iowa City, Iowa 52242, United States
| | - Jessica M. Ewald
- Department of Civil and Environmental
Engineering, 4105 Seamans Center, University
of Iowa, Iowa City, Iowa 52242, United States
| | - Timothy E. Mattes
- Department of Civil and Environmental
Engineering, 4105 Seamans Center, University
of Iowa, Iowa City, Iowa 52242, United States
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Kumari S, Das S. Bacterial enzymatic degradation of recalcitrant organic pollutants: catabolic pathways and genetic regulations. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:79676-79705. [PMID: 37330441 DOI: 10.1007/s11356-023-28130-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 06/01/2023] [Indexed: 06/19/2023]
Abstract
Contamination of soil and natural water bodies driven by increased organic pollutants remains a universal concern. Naturally, organic pollutants contain carcinogenic and toxic properties threatening all known life forms. The conventional physical and chemical methods employed to remove these organic pollutants ironically produce toxic and non-ecofriendly end-products. Whereas microbial-based degradation of organic pollutants provides an edge, they are usually cost-effective and take an eco-friendly approach towards remediation. Bacterial species, including Pseudomonas, Comamonas, Burkholderia, and Xanthomonas, have the unique genetic makeup to metabolically degrade toxic pollutants, conferring their survival in toxic environments. Several catabolic genes, such as alkB, xylE, catA, and nahAc, that encode enzymes and allow bacteria to degrade organic pollutants have been identified, characterized, and even engineered for better efficacy. Aerobic and anaerobic processes are followed by bacteria to metabolize aliphatic saturated and unsaturated hydrocarbons such as alkanes, cycloalkanes, aldehydes, and ethers. Bacteria use a variety of degrading pathways, including catechol, protocatechuate, gentisate, benzoate, and biphenyl, to remove aromatic organic contaminants such as polychlorinated biphenyls, polycyclic aromatic hydrocarbons, and pesticides from the environment. A better understanding of the principle, mechanisms, and genetics would be beneficial for improving the metabolic efficacy of bacteria to such ends. With a focus on comprehending the mechanisms involved in various catabolic pathways and the genetics of the biotransformation of these xenobiotic compounds, the present review offers insight into the various sources and types of known organic pollutants and their toxic effects on health and the environment.
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Affiliation(s)
- Swetambari Kumari
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, 769008, Odisha, India
| | - Surajit Das
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, 769008, Odisha, India.
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