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Hasan MK, Jeannine Brady L. Nucleic acid-binding KH domain proteins influence a spectrum of biological pathways including as part of membrane-localized complexes. J Struct Biol X 2024; 10:100106. [PMID: 39040530 PMCID: PMC11261784 DOI: 10.1016/j.yjsbx.2024.100106] [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: 02/23/2024] [Revised: 06/18/2024] [Accepted: 06/24/2024] [Indexed: 07/24/2024] Open
Abstract
K-Homology domain (KH domain) proteins bind single-stranded nucleic acids, influence protein-protein interactions of proteins that harbor them, and are found in all kingdoms of life. In concert with other functional protein domains KH domains contribute to a variety of critical biological activities, often within higher order machineries including membrane-localized protein complexes. Eukaryotic KH domain proteins are linked to developmental processes, morphogenesis, and growth regulation, and their aberrant expression is often associated with cancer. Prokaryotic KH domain proteins are involved in integral cellular activities including cell division and protein translocation. Eukaryotic and prokaryotic KH domains share structural features, but are differentiated based on their structural organizations. In this review, we explore the structure/function relationships of known examples of KH domain proteins, and highlight cases in which they function within or at membrane surfaces. We also summarize examples of KH domain proteins that influence bacterial virulence and pathogenesis. We conclude the article by discussing prospective research avenues that could be pursued to better investigate this largely understudied protein category.
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Affiliation(s)
- Md Kamrul Hasan
- Department of Oral Biology, University of Florida, Gainesville, FL 32610, USA
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - L. Jeannine Brady
- Department of Oral Biology, University of Florida, Gainesville, FL 32610, USA
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2
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Morrison JJ, Madden EK, Banas DA, DiBiasio EC, Hansen M, Krogfelt KA, Rowley DC, Cohen PS, Camberg JL. Metabolic flux regulates growth transitions and antibiotic tolerance in uropathogenic Escherichia coli. J Bacteriol 2024; 206:e0016224. [PMID: 38814092 PMCID: PMC11332148 DOI: 10.1128/jb.00162-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Accepted: 05/06/2024] [Indexed: 05/31/2024] Open
Abstract
Reducing growth and limiting metabolism are strategies that allow bacteria to survive exposure to environmental stress and antibiotics. During infection, uropathogenic Escherichia coli (UPEC) may enter a quiescent state that enables them to reemerge after the completion of successful antibiotic treatment. Many clinical isolates, including the well-characterized UPEC strain CFT073, also enter a metabolite-dependent, quiescent state in vitro that is reversible with cues, including peptidoglycan-derived peptides and amino acids. Here, we show that quiescent UPEC is antibiotic tolerant and demonstrate that metabolic flux in the tricarboxylic acid (TCA) cycle regulates the UPEC quiescent state via succinyl-CoA. We also demonstrate that the transcriptional regulator complex integration host factor and the FtsZ-interacting protein ZapE, which is important for E. coli division during stress, are essential for UPEC to enter the quiescent state. Notably, in addition to engaging FtsZ and late-stage cell division proteins, ZapE also interacts directly with TCA cycle enzymes in bacterial two-hybrid assays. We report direct interactions between the succinate dehydrogenase complex subunit SdhC, the late-stage cell division protein FtsN, and ZapE. These interactions may enable communication between oxidative metabolism and the cell division machinery in UPEC. Moreover, these interactions are conserved in an E. coli K-12 strain. This work suggests that there is coordination among the two fundamental and essential pathways that regulate overall growth, quiescence, and antibiotic susceptibility. IMPORTANCE Uropathogenic Escherichia coli (UPEC) are the leading cause of urinary tract infections (UTIs). Upon invasion into bladder epithelial cells, UPEC establish quiescent intracellular reservoirs that may lead to antibiotic tolerance and recurrent UTIs. Here, we demonstrate using an in vitro system that quiescent UPEC cells are tolerant to ampicillin and have decreased metabolism characterized by succinyl-CoA limitation. We identify the global regulator integration host factor complex and the cell division protein ZapE as critical modifiers of quiescence and antibiotic tolerance. Finally, we show that ZapE interacts with components of both the cell division machinery and the tricarboxylic acid cycle, and this interaction is conserved in non-pathogenic E. coli, establishing a novel link between cell division and metabolism.
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Affiliation(s)
- Josiah J. Morrison
- Department of Cell and Molecular Biology, The University of Rhode Island, Kingston, Rhode Island, USA
| | - Ellen K. Madden
- Department of Cell and Molecular Biology, The University of Rhode Island, Kingston, Rhode Island, USA
| | - Daniel A. Banas
- Department of Cell and Molecular Biology, The University of Rhode Island, Kingston, Rhode Island, USA
| | - Eric C. DiBiasio
- Department of Cell and Molecular Biology, The University of Rhode Island, Kingston, Rhode Island, USA
| | - Mads Hansen
- Department of Natural Science and Environment, Centre for Mathematical Modeling - Human Health and Disease, University of Roskilde, Roskilde, Denmark
| | - Karen A. Krogfelt
- Department of Natural Science and Environment, Centre for Mathematical Modeling - Human Health and Disease, University of Roskilde, Roskilde, Denmark
| | - David C. Rowley
- Department of Biomedical and Pharmaceutical Sciences, The University of Rhode Island, Kingston, Rhode Island, USA
| | - Paul S. Cohen
- Department of Cell and Molecular Biology, The University of Rhode Island, Kingston, Rhode Island, USA
| | - Jodi L. Camberg
- Department of Cell and Molecular Biology, The University of Rhode Island, Kingston, Rhode Island, USA
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Radler P, Loose M. A dynamic duo: Understanding the roles of FtsZ and FtsA for Escherichia coli cell division through in vitro approaches. Eur J Cell Biol 2024; 103:151380. [PMID: 38218128 DOI: 10.1016/j.ejcb.2023.151380] [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: 07/25/2023] [Revised: 12/22/2023] [Accepted: 12/24/2023] [Indexed: 01/15/2024] Open
Abstract
Bacteria divide by binary fission. The protein machine responsible for this process is the divisome, a transient assembly of more than 30 proteins in and on the surface of the cytoplasmic membrane. Together, they constrict the cell envelope and remodel the peptidoglycan layer to eventually split the cell into two. For Escherichia coli, most molecular players involved in this process have probably been identified, but obtaining the quantitative information needed for a mechanistic understanding can often not be achieved from experiments in vivo alone. Since the discovery of the Z-ring more than 30 years ago, in vitro reconstitution experiments have been crucial to shed light on molecular processes normally hidden in the complex environment of the living cell. In this review, we summarize how rebuilding the divisome from purified components - or at least parts of it - have been instrumental to obtain the detailed mechanistic understanding of the bacterial cell division machinery that we have today.
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Affiliation(s)
- Philipp Radler
- Institute for Science and Technology Austria (ISTA), Am Campus 1, 3400 Klosterneuburg, Austria; University of Vienna, Djerassiplatz 1, 1030 Wien, Austria.
| | - Martin Loose
- Institute for Science and Technology Austria (ISTA), Am Campus 1, 3400 Klosterneuburg, Austria.
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Morrison JJ, Camberg JL. Building the Bacterial Divisome at the Septum. Subcell Biochem 2024; 104:49-71. [PMID: 38963483 DOI: 10.1007/978-3-031-58843-3_4] [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: 07/05/2024]
Abstract
Across living organisms, division is necessary for cell survival and passing heritable information to the next generation. For this reason, cell division is highly conserved among eukaryotes and prokaryotes. Among the most highly conserved cell division proteins in eukaryotes are tubulin and actin. Tubulin polymerizes to form microtubules, which assemble into cytoskeletal structures in eukaryotes, such as the mitotic spindle that pulls chromatids apart during mitosis. Actin polymerizes to form a morphological framework for the eukaryotic cell, or cytoskeleton, that undergoes reorganization during mitosis. In prokaryotes, two of the most highly conserved cell division proteins are the tubulin homolog FtsZ and the actin homolog FtsA. In this chapter, the functions of the essential bacterial cell division proteins FtsZ and FtsA and their roles in assembly of the divisome at the septum, the site of cell division, will be discussed. In most bacteria, including Escherichia coli, the tubulin homolog FtsZ polymerizes at midcell, and this step is crucial for recruitment of many other proteins to the division site. For this reason, both FtsZ abundance and polymerization are tightly regulated by a variety of proteins. The actin-like FtsA protein polymerizes and tethers FtsZ polymers to the cytoplasmic membrane. Additionally, FtsA interacts with later stage cell division proteins, which are essential for division and for building the new cell wall at the septum. Recent studies have investigated how actin-like polymerization of FtsA on the lipid membrane may impact division, and we will discuss this and other ways that division in bacteria is regulated through FtsZ and FtsA.
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Affiliation(s)
- Josiah J Morrison
- Department of Cell and Molecular Biology, The University of Rhode Island, Kingston, RI, USA
| | - Jodi L Camberg
- Department of Cell and Molecular Biology, The University of Rhode Island, Kingston, RI, USA.
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Naha A, Haeusser DP, Margolin W. Anchors: A way for FtsZ filaments to stay membrane bound. Mol Microbiol 2023; 120:525-538. [PMID: 37503768 PMCID: PMC10593102 DOI: 10.1111/mmi.15067] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/10/2023] [Accepted: 04/12/2023] [Indexed: 07/29/2023]
Abstract
Most bacteria use the tubulin homolog FtsZ to organize their cell division. FtsZ polymers initially assemble into mobile complexes that circle around a ring-like structure at the cell midpoint, followed by the recruitment of other proteins that will constrict the cytoplasmic membrane and synthesize septal peptidoglycan to divide the cell. Despite the need for FtsZ polymers to associate with the membrane, FtsZ lacks intrinsic membrane binding ability. Consequently, FtsZ polymers have evolved to interact with the membrane through adaptor proteins that both bind FtsZ and the membrane. Here, we discuss recent progress in understanding the functions of these FtsZ membrane tethers. Some, such as FtsA and SepF, are widely conserved and assemble into varied oligomeric structures bound to the membrane through an amphipathic helix. Other less-conserved proteins, such as EzrA and ZipA, have transmembrane domains, make extended structures, and seem to bind to FtsZ through two separate interactions. This review emphasizes that most FtsZs use multiple membrane tethers with overlapping functions, which not only attach FtsZ polymers to the membrane but also organize them in specific higher-order structures that can optimize cell division activity. We discuss gaps in our knowledge of these concepts and how future studies can address them.
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Affiliation(s)
- Arindam Naha
- Department of Microbiology and Molecular Genetics, UTHealth-Houston, Houston, TX 77030, USA
| | - Daniel P. Haeusser
- Department of Microbiology and Molecular Genetics, UTHealth-Houston, Houston, TX 77030, USA
- Department of Biology, Canisius College, Buffalo, NY 14208, USA
| | - William Margolin
- Department of Microbiology and Molecular Genetics, UTHealth-Houston, Houston, TX 77030, USA
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Peng J, Dai X, Fan H, Xing C, Zhuang Y, Gao X, Cao H, Hu G, Yang F. Mitochondria-associated endoplasmic reticulum membranes participate mitochondrial dysfunction and endoplasmic reticulum stress caused by copper in duck kidney. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023:10.1007/s11356-023-27924-z. [PMID: 37253910 DOI: 10.1007/s11356-023-27924-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 05/22/2023] [Indexed: 06/01/2023]
Abstract
Copper (Cu) can be harmful to host physiology at high levels, although it is still unclear exactly how it causes nephrotoxicity. Mitochondrial dysfunction and endoplasmic reticulum (ER) stress are associated with heavy metal intoxication. Meanwhile, mitochondria and ER are connected via mitochondria-associated ER membranes (MAM). In order to reveal the crosstalk between them, a total of 144 1-day-old Peking ducks were randomly divided into four groups: control (basal diet), 100 mg/kg Cu, 200 mg/kg Cu, and 400 mg/kg Cu groups. Results found that excessive Cu disrupted MAM integrity, reduced the co-localization of IP3R and VDAC1, and significantly changed the MAM-related factors levels (Grp75, Mfn2, IP3R, MCU, PACS2, and VDAC1), leading to MAM dysfunction. We further found that Cu exposure induced mitochondrial dysfunction via decreasing the ATP level and the expression levels of COX4, TOM20, SIRT1, and OPA1 and up-regulating Parkin expression level. Meanwhile, Cu exposure dramatically increased the expression levels of Grp78, CRT, and ATF4, resulting in ER stress. Overall, these findings demonstrated MAM plays the critical role in Cu-induced kidney mitochondrial dysfunction and ER stress, which deepened our understanding of Cu-induced nephrotoxicity.
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Affiliation(s)
- Junjun Peng
- Jiangxi Provincial Key Laboratory for Animal Health, Institute of Animal Population Health, College of Animal Science and Technology, Economic and Technological Development District, Jiangxi Agricultural University, No. 1101 Zhimin Avenue, Nanchang, 330045, Jiangxi, People's Republic of China
| | - Xueyan Dai
- Jiangxi Provincial Key Laboratory for Animal Health, Institute of Animal Population Health, College of Animal Science and Technology, Economic and Technological Development District, Jiangxi Agricultural University, No. 1101 Zhimin Avenue, Nanchang, 330045, Jiangxi, People's Republic of China
| | - Huiqin Fan
- Jiangxi Provincial Key Laboratory for Animal Health, Institute of Animal Population Health, College of Animal Science and Technology, Economic and Technological Development District, Jiangxi Agricultural University, No. 1101 Zhimin Avenue, Nanchang, 330045, Jiangxi, People's Republic of China
| | - Chenghong Xing
- Jiangxi Provincial Key Laboratory for Animal Health, Institute of Animal Population Health, College of Animal Science and Technology, Economic and Technological Development District, Jiangxi Agricultural University, No. 1101 Zhimin Avenue, Nanchang, 330045, Jiangxi, People's Republic of China
| | - Yu Zhuang
- Jiangxi Provincial Key Laboratory for Animal Health, Institute of Animal Population Health, College of Animal Science and Technology, Economic and Technological Development District, Jiangxi Agricultural University, No. 1101 Zhimin Avenue, Nanchang, 330045, Jiangxi, People's Republic of China
| | - Xiaona Gao
- Jiangxi Provincial Key Laboratory for Animal Health, Institute of Animal Population Health, College of Animal Science and Technology, Economic and Technological Development District, Jiangxi Agricultural University, No. 1101 Zhimin Avenue, Nanchang, 330045, Jiangxi, People's Republic of China
| | - Huabin Cao
- Jiangxi Provincial Key Laboratory for Animal Health, Institute of Animal Population Health, College of Animal Science and Technology, Economic and Technological Development District, Jiangxi Agricultural University, No. 1101 Zhimin Avenue, Nanchang, 330045, Jiangxi, People's Republic of China
| | - Guoliang Hu
- Jiangxi Provincial Key Laboratory for Animal Health, Institute of Animal Population Health, College of Animal Science and Technology, Economic and Technological Development District, Jiangxi Agricultural University, No. 1101 Zhimin Avenue, Nanchang, 330045, Jiangxi, People's Republic of China
| | - Fan Yang
- Jiangxi Provincial Key Laboratory for Animal Health, Institute of Animal Population Health, College of Animal Science and Technology, Economic and Technological Development District, Jiangxi Agricultural University, No. 1101 Zhimin Avenue, Nanchang, 330045, Jiangxi, People's Republic of China.
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Morrison JJ, Ferreira CN, Siler EM, Nelson K, Trebino CE, Piraino B, Camberg JL. Nucleotide-dependent activities of FtsA regulate the early establishment of a functional divisome during the Escherichia coli cell cycle. Front Microbiol 2023; 14:1171376. [PMID: 37250038 PMCID: PMC10213515 DOI: 10.3389/fmicb.2023.1171376] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 04/24/2023] [Indexed: 05/31/2023] Open
Abstract
During cell division in Escherichia coli, the highly conserved tubulin homolog FtsZ polymerizes and assembles into a ring-like structure, called the Z-ring, at the site of septation. For recruitment to the membrane surface, FtsZ polymers directly interact with membrane-associated proteins, predominantly FtsA in E. coli. FtsA shares structural homology with actin and, like actin, hydrolyzes ATP. Yeast actin detects nucleotide occupancy through a sensor region adjacent to the nucleotide binding site and adopts distinct conformations in monomeric and filamentous actin. Bacterial actin homologs also display considerable conformational flexibility across different nucleotide-bound states and polymerize. Here, we show that several amino acid residues proximal to the nucleotide binding site in FtsA are critical for function in vitro and in vivo. Each of these residues are important for ATP hydrolysis, phospholipid (PL) binding, ATP-dependent vesicle remodeling, and recruitment to the divisome in vivo, to varying degrees. Notably, we observed that Ser 84 and Glu 14 are essential for ATP-dependent vesicle remodeling and magnesium-dependent membrane release of FtsA from vesicles in vitro, and these defects likely underlie the loss of function by FtsA(E14R) and FtsA(S84L) in vivo. Finally, we demonstrate that FtsA(A188V), which is associated with temperature-sensitive growth in vivo, is defective for rapid ATP hydrolysis and ATP-dependent remodeling of PL vesicles in vitro. Together, our results show that loss of nucleotide-dependent activities by FtsA, such as ATP hydrolysis, membrane binding and release, and, most importantly, ATP-dependent PL remodeling, lead to failed Z-ring assembly and division defects in cells.
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Gurnani M, Chauhan A, Ranjan A, Tuli HS, Alkhanani MF, Haque S, Dhama K, Lal R, Jindal T. Filamentous Thermosensitive Mutant Z: An Appealing Target for Emerging Pathogens and a Trek on Its Natural Inhibitors. BIOLOGY 2022; 11:biology11050624. [PMID: 35625352 PMCID: PMC9138142 DOI: 10.3390/biology11050624] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 03/18/2022] [Accepted: 04/01/2022] [Indexed: 12/14/2022]
Abstract
Simple Summary Antimicrobial resistance (AMR) is a pressing issue worldwide that must be addressed swiftly. It is driven by spontaneous evolution, bacterial mutation, and the dissemination of resistant genes via horizontal gene transfer. Researchers are working on many novel targets, which can become a pathway to inhibit harmful bacteria. Filamentous Thermosensitive mutant-Z (Fts-Z) is one such bacterial target that has gained popularity amongst scientists due to its conserved nature in bacteria and absence in eukaryotes. The aim of this work was to review the Fts-Z mechanism of action along with current studies on natural inhibitors for Fts-Z. Abstract Antibiotic resistance is a major emerging issue in the health care sector, as highlighted by the WHO. Filamentous Thermosensitive mutant Z (Fts-Z) is gaining significant attention in the scientific community as a potential anti-bacterial target for fighting antibiotic resistance among several pathogenic bacteria. The Fts-Z plays a key role in bacterial cell division by allowing Z ring formation. Several in vitro and in silico experiments have demonstrated that inhibition of Fts-Z can lead to filamentous growth of the cells, and finally, cell death occurs. Many natural compounds that have successfully inhibited Fts-Z are also studied. This review article intended to highlight the structural–functional aspect of Fts-Z that leads to Z-ring formation and its contribution to the biochemistry and physiology of cells. The current trend of natural inhibitors of Fts-Z protein is also covered.
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Affiliation(s)
- Manisha Gurnani
- Amity Institute of Environmental Science, Amity University, Noida 201301, India;
| | - Abhishek Chauhan
- Amity Institute of Environmental Toxicology, Safety and Management, Amity University, Noida 201303, India;
- Correspondence: (A.C.); (A.R.)
| | - Anuj Ranjan
- Academy of Biology and Biotechnology, Southern Federal University, 344006 Rostov-on-Don, Russia
- Correspondence: (A.C.); (A.R.)
| | - Hardeep Singh Tuli
- Department of Biotechnology, Maharishi Markandeshwar (Deemed to be University), Ambala 133207, India;
| | - Mustfa F. Alkhanani
- Emergency Service Department, College of Applied Sciences, AlMaarefa University, Riyadh 11597, Saudi Arabia;
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan 45142, Saudi Arabia;
- Faculty of Medicine, Görükle Campus, Bursa Uludağ University, Nilüfer, Bursa 16059, Turkey
| | - Kuldeep Dhama
- Division of Pathology, ICAR—Indian Veterinary Research Institute, Bareilly 243122, India;
| | - Rup Lal
- Department of Zoology, University of Delhi, Delhi 110021, India;
| | - Tanu Jindal
- Amity Institute of Environmental Toxicology, Safety and Management, Amity University, Noida 201303, India;
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