1
|
Dowhan W, Bogdanov M. Eugene P. Kennedy's Legacy: Defining Bacterial Phospholipid Pathways and Function. Front Mol Biosci 2021; 8:666203. [PMID: 33842554 PMCID: PMC8027125 DOI: 10.3389/fmolb.2021.666203] [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: 02/09/2021] [Accepted: 03/01/2021] [Indexed: 12/27/2022] Open
Abstract
In the 1950's and 1960's Eugene P. Kennedy laid out the blueprint for phospholipid biosynthesis in somatic cells and Escherichia coli, which have been coined the Kennedy Pathways for phospholipid biosynthesis. His research group continued to make seminal contributions in the area of phospholipids until his retirement in the early 1990's. During these years he mentored many young scientists that continued to build on his early discoveries and who also mentored additional scientists that continue to make important contributions in areas related to phospholipids and membrane biogenesis. This review will focus on the initial E. coli Kennedy Pathways and how his early contributions have laid the foundation for our current understanding of bacterial phospholipid genetics, biochemistry and function as carried on by his scientific progeny and others who have been inspired to study microbial phospholipids.
Collapse
Affiliation(s)
- William Dowhan
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center, Houston, TX, United States
| | - Mikhail Bogdanov
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center, Houston, TX, United States
| |
Collapse
|
2
|
López-Lara IM, Geiger O. Bacterial lipid diversity. Biochim Biophys Acta Mol Cell Biol Lipids 2017; 1862:1287-1299. [DOI: 10.1016/j.bbalip.2016.10.007] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2016] [Revised: 10/10/2016] [Accepted: 10/11/2016] [Indexed: 11/25/2022]
|
3
|
Vimala A, Harinarayanan R. Transketolase activity modulates glycerol-3-phosphate levels inEscherichia coli. Mol Microbiol 2016; 100:263-77. [DOI: 10.1111/mmi.13317] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/16/2015] [Indexed: 11/30/2022]
Affiliation(s)
- A. Vimala
- Laboratory of Bacterial Genetics; Center for DNA Fingerprinting and Diagnostics; Hyderabad 500 001 India
| | - R. Harinarayanan
- Laboratory of Bacterial Genetics; Center for DNA Fingerprinting and Diagnostics; Hyderabad 500 001 India
| |
Collapse
|
4
|
Abstract
The pathways in Escherichia coli and (largely by analogy) S. enterica remain the paradigm of bacterial lipid synthetic pathways, although recently considerable diversity among bacteria in the specific areas of lipid synthesis has been demonstrated. The structural biology of the fatty acid synthetic proteins is essentially complete. However, the membrane-bound enzymes of phospholipid synthesis remain recalcitrant to structural analyses. Recent advances in genetic technology have allowed the essentialgenes of lipid synthesis to be tested with rigor, and as expected most genes are essential under standard growth conditions. Conditionally lethal mutants are available in numerous genes, which facilitates physiological analyses. The array of genetic constructs facilitates analysis of the functions of genes from other organisms. Advances in mass spectroscopy have allowed very accurate and detailed analyses of lipid compositions as well as detection of the interactions of lipid biosynthetic proteins with one another and with proteins outside the lipid pathway. The combination of these advances has resulted in use of E. coli and S. enterica for discovery of new antimicrobials targeted to lipid synthesis and in deciphering the molecular actions of known antimicrobials. Finally,roles for bacterial fatty acids other than as membrane lipid structural components have been uncovered. For example, fatty acid synthesis plays major roles in the synthesis of the essential enzyme cofactors, biotin and lipoic acid. Although other roles for bacterial fatty acids, such as synthesis of acyl-homoserine quorum-sensing molecules, are not native to E. coli introduction of the relevant gene(s) synthesis of these foreign molecules readily proceeds and the sophisticated tools available can used to decipher the mechanisms of synthesis of these molecules.
Collapse
|
5
|
Nikel PI, Kim J, de Lorenzo V. Metabolic and regulatory rearrangements underlying glycerol metabolism inPseudomonas putida KT2440. Environ Microbiol 2013; 16:239-54. [DOI: 10.1111/1462-2920.12224] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Revised: 07/12/2013] [Accepted: 07/20/2013] [Indexed: 11/28/2022]
Affiliation(s)
- Pablo I. Nikel
- Systems and Synthetic Biology Program; Centro Nacional de Biotecnología (CNB-CSIC); Madrid 28049 Spain
| | - Juhyun Kim
- Systems and Synthetic Biology Program; Centro Nacional de Biotecnología (CNB-CSIC); Madrid 28049 Spain
| | - Víctor de Lorenzo
- Systems and Synthetic Biology Program; Centro Nacional de Biotecnología (CNB-CSIC); Madrid 28049 Spain
| |
Collapse
|
6
|
Dowhan W. A retrospective: use of Escherichia coli as a vehicle to study phospholipid synthesis and function. BIOCHIMICA ET BIOPHYSICA ACTA 2013; 1831:471-94. [PMID: 22925633 PMCID: PMC3513495 DOI: 10.1016/j.bbalip.2012.08.007] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2012] [Revised: 08/07/2012] [Accepted: 08/07/2012] [Indexed: 12/11/2022]
Abstract
Although the study of individual phospholipids and their synthesis began in the 1920s first in plants and then mammals, it was not until the early 1960s that Eugene Kennedy using Escherichia coli initiated studies of bacterial phospholipid metabolism. With the base of information already available from studies of mammalian tissue, the basic blueprint of phospholipid biosynthesis in E. coli was worked out by the late 1960s. In 1970s and 1980s most of the enzymes responsible for phospholipid biosynthesis were purified and many of the genes encoding these enzymes were identified. By the late 1990s conditional and null mutants were available along with clones of the genes for every step of phospholipid biosynthesis. Most of these genes had been sequenced before the complete E. coli genome sequence was available. Strains of E. coli were developed in which phospholipid composition could be changed in a systematic manner while maintaining cell viability. Null mutants, strains in which phospholipid metabolism was artificially regulated, and strains synthesizing foreign lipids not found in E. coli have been used to this day to define specific roles for individual phospholipid. This review will trace the findings that have led to the development of E. coli as an excellent model system to study mechanisms underlying the synthesis and function of phospholipids that are widely applicable to other prokaryotic and eukaryotic systems. This article is part of a Special Issue entitled Phospholipids and Phospholipid Metabolism.
Collapse
Affiliation(s)
- William Dowhan
- Department of Biochemistry and Molecular Biology, University of Texas Medical School-Houston, Houston, TX 77030, USA.
| |
Collapse
|
7
|
Large mutational target size for rapid emergence of bacterial persistence. Proc Natl Acad Sci U S A 2012; 109:12740-5. [PMID: 22802628 DOI: 10.1073/pnas.1205124109] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Phenotypic heterogeneity displayed by a clonal bacterial population permits a small fraction of cells to survive prolonged exposure to antibiotics. Although first described over 60 y ago, the molecular mechanisms underlying this behavior, termed persistence, remain largely unknown. To systematically explore the genetic basis of persistence, we selected a library of transposon-mutagenized Escherichia coli cells for survival to multiple rounds of lethal ampicillin exposure. Application of microarray-based genetic footprinting revealed a large number of loci that drastically elevate persistence frequency through null mutations and domain disruptions. In one case, the C-terminal disruption of methionyl-tRNA synthetase (MetG) results in a 10,000-fold higher persistence frequency than wild type. We discovered a mechanism by which null mutations in transketolase A (tktA) and glycerol-3-phosphate (G3P) dehydrogenase (glpD) increase persistence through metabolic flux alterations that increase intracellular levels of the growth-inhibitory metabolite methylglyoxal. Systematic double-mutant analyses revealed the genetic network context in which such persistent mutants function. Our findings reveal a large mutational target size for increasing persistence frequency, which has fundamental implications for the emergence of antibiotic tolerance in the clinical setting.
Collapse
|
8
|
Rickettsia prowazekii uses an sn-glycerol-3-phosphate dehydrogenase and a novel dihydroxyacetone phosphate transport system to supply triose phosphate for phospholipid biosynthesis. J Bacteriol 2010; 192:4281-8. [PMID: 20581209 DOI: 10.1128/jb.00443-10] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Rickettsia prowazekii is an obligate intracellular pathogen that possesses a small genome and a highly refined repertoire of biochemical pathways compared to those of free-living bacteria. Here we describe a novel biochemical pathway that relies on rickettsial transport of host cytosolic dihydroxyacetone phosphate (DHAP) and its subsequent conversion to sn-glycerol-3-phosphate (G3P) for synthesis of phospholipids. This rickettsial pathway compensates for the evolutionary loss of rickettsial glycolysis/gluconeogenesis, the typical endogenous source of G3P. One of the components of this pathway is R. prowazekii open reading frame RP442, which is annotated GpsA, a G3P dehydrogenase (G3PDH). Purified recombinant rickettsial GpsA was shown to specifically catalyze the conversion of DHAP to G3P in vitro. The products of the GpsA assay were monitored spectrophotometrically, and the identity of the reaction product was verified by paper chromatography. In addition, heterologous expression of the R. prowazekii gpsA gene functioned to complement an Escherichia coli gpsA mutant. Furthermore, gpsA mRNA was detected in R. prowazekii purified from hen egg yolk sacs, and G3PDH activity was assayable in R. prowazekii lysed-cell extracts. Together, these data strongly suggested that R. prowazekii encodes and synthesizes a functional GpsA enzyme, yet R. prowazekii is unable to synthesize DHAP as a substrate for the GpsA enzymatic reaction. On the basis of the fact that intracellular organisms often avail themselves of resources in the host cell cytosol via the activity of novel carrier-mediated transport systems, we reasoned that R. prowazekii transports DHAP to supply substrate for GpsA. In support of this hypothesis, we show that purified R. prowazekii transported and incorporated DHAP into phospholipids, thus implicating a role for GpsA in vivo as part of a novel rickettsial G3P acquisition pathway for phospholipid biosynthesis.
Collapse
|
9
|
Xavier KB, Bassler BL. Regulation of uptake and processing of the quorum-sensing autoinducer AI-2 in Escherichia coli. J Bacteriol 2005; 187:238-48. [PMID: 15601708 PMCID: PMC538819 DOI: 10.1128/jb.187.1.238-248.2005] [Citation(s) in RCA: 310] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
AI-2 is a quorum-sensing signaling molecule proposed to be involved in interspecies communication. In Escherichia coli and Salmonella enterica serovar Typhimurium, extracellular AI-2 accumulates in exponential phase, but the amount decreases drastically upon entry into stationary phase. In S. enterica serovar Typhimurium, the reduction in activity is due to import and processing of AI-2 by the Lsr transporter. We show that the Lsr transporter is functional in E. coli, and screening for mutants defective in AI-2 internalization revealed lsrK and glpD. Unlike the wild type, lsrK and glpD mutants do not activate transcription of the lsr operon in response to AI-2. lsrK encodes the AI-2 kinase, and the lsrK mutant fails to activate lsr expression because it cannot produce phospho-AI-2, which is the lsr operon inducer. glpD encodes the glycerol-3-phosphate (G3P) dehydrogenase, which is involved in glycerol and G3P metabolism. G3P accumulates in the glpD mutant and represses lsr transcription by preventing cyclic AMP (cAMP)-catabolite activator protein (CAP)-dependent activation. Dihydroxyacetone phosphate (DHAP) also accumulates in the glpD mutant, and DHAP represses lsr transcription by a cAMP-CAP-independent mechanism involving LsrR, the lsr operon repressor. The requirement for cAMP-CAP in lsr activation explains why AI-2 persists in culture fluids of bacteria grown in media containing sugars that cause catabolite repression. These findings show that, depending on the prevailing growth conditions, the amount of time that the AI-2 signal is present and, in turn, the time that a given community of bacteria remains exposed to this signal can vary greatly.
Collapse
Affiliation(s)
- Karina B Xavier
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544-1014, USA
| | | |
Collapse
|
10
|
Abstract
Phospholipids play multiple roles in bacterial cells. These are the establishment of the permeability barrier, provision of the environment for many enzyme and transporter proteins, and they influence membrane-related processes such as protein export and DNA replication. The lipid synthetic pathway also provides precursors for protein modification and for the synthesis of other molecules. This review concentrates on the phospholipid synthetic pathway and discusses recent data on the synthesis and function of phospholipids mainly in the bacterium Escherichia coli.
Collapse
Affiliation(s)
- John E Cronan
- Department of Microbiology, University of Illinois, Urbana, Illinois 61801, USA.
| |
Collapse
|
11
|
|
12
|
Abstract
Extensive genetic and biochemical studies in the last two decades have elucidated almost completely the framework of synthesis and turnover of quantitatively major phospholipids in E. coli. The knowledge thus accumulated has allowed to formulate a novel working model that assumes sophisticated regulatory mechanisms in E. coli to achieve the optimal phospholipid composition and content in the membranes. E. coli also appears to possess the ability to adapt phospholipid synthesis to various cellular conditions. Understanding of the functional aspects of E. coli phospholipids is now advancing significantly and it will soon be able to explain many of the hitherto unclear cell's activities on the molecular basis. Phosphatidylglycerol is believed to play the central role both in metabolism and functions of phospholipids in E. coli. The results obtained with E. coli should undoubtedly be helpful in the study of more complicated phospholipid metabolism and functions in higher organisms.
Collapse
Affiliation(s)
- I Shibuya
- Department of Biochemistry, Saitama University, Urawa, Japan
| |
Collapse
|
13
|
Kumamoto CA. SecB protein: a cytosolic export factor that associates with nascent exported proteins. J Bioenerg Biomembr 1990; 22:337-51. [PMID: 2202722 DOI: 10.1007/bf00763171] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Soluble factors participate in protein translocation across a variety of biological membranes. The Escherichia coli soluble protein SecB (the product of the secB gene) is involved in the export of periplasmic and outer membrane proteins. The isolation of secB mutations permitted the demonstration that SecB is required for rapid and efficient export of certain proteins. Consistent with the results of these genetic studies, purified SecB has been shown to stimulate protein translocation across E. coli inner membrane vesicles in vitro. This article presents a review of these past studies of SecB, speculation on the role of SecB in protein translocation, and a comparison of SecB and other factors, trigger factor and GroEL.
Collapse
Affiliation(s)
- C A Kumamoto
- Department of Physiology, Tufts University School of Medicine, Boston, Massachusetts 02111
| |
Collapse
|
14
|
Abstract
The Escherichia coli secB gene product is required for normal export of envelope proteins out of the cell cytoplasm. In this report, we present the identification and nucleotide sequence of the secB coding sequence. The secB structural gene overlaps almost completely with a predicted open reading frame (ORF) that is encoded on the opposite strand. To establish the identity of the secB ORF, we characterized a secB mutation that caused total loss of secB function, based upon its phenotype. This mutation resulted from a nucleotide change that caused an ochre mutation in one ORF (the secB gene) and a silent (no amino acid change) codon change in the opposite ORF.
Collapse
Affiliation(s)
- C A Kumamoto
- Department of Physiology, Tufts University School of Medicine, Boston, MA 02111
| | | |
Collapse
|
15
|
Kumamoto CA, Beckwith J. Evidence for specificity at an early step in protein export in Escherichia coli. J Bacteriol 1985; 163:267-74. [PMID: 3891730 PMCID: PMC219108 DOI: 10.1128/jb.163.1.267-274.1985] [Citation(s) in RCA: 234] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
We previously described mutations in a gene, secB, which have pleiotropic effects on protein export in Escherichia coli. In this paper, we report the isolation of mutants in which the activity of the secB gene was eliminated. Null mutations in secB affected only a subset of exported proteins. Strains carrying these mutations, although unable to grow on L broth plates, were still viable on minimal media. These secB mutations reversed a block in the translation of an exported protein that was caused by the elimination of another component of the secretion machinery, SecA protein. These results suggest that the secB product acts at an early step in the export process and is involved in the export of only a subset of cell envelope proteins.
Collapse
|
16
|
8 Formation of Bacterial Glycerolipids. ACTA ACUST UNITED AC 1983. [DOI: 10.1016/s1874-6047(08)60306-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
|
17
|
Chapter 11 Genetic control of phospholipid bilayer assembly. ACTA ACUST UNITED AC 1982. [DOI: 10.1016/s0167-7306(08)60015-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
|
18
|
Regulation of Bacterial Membrane Lipid Synthesis. ACTA ACUST UNITED AC 1982. [DOI: 10.1016/s0070-2161(08)60312-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
|
19
|
Membrane phospholipid synthesis in Escherichia coli. Purification, reconstitution, and characterization of sn-glycerol-3-phosphate acyltransferase. J Biol Chem 1981. [DOI: 10.1016/s0021-9258(19)68570-4] [Citation(s) in RCA: 105] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
|
20
|
Ohta A, Waggoner K, Radominska-Pyrek A, Dowhan W. Cloning of genes involved in membrane lipid synthesis: effects of amplification of phosphatidylglycerophosphate synthase in Escherichia coli. J Bacteriol 1981; 147:552-62. [PMID: 6267013 PMCID: PMC216076 DOI: 10.1128/jb.147.2.552-562.1981] [Citation(s) in RCA: 57] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The structural gene (pgsA) for the CDP-diacylglycerol:sn-glycero-3-phosphate phosphatidyltransferase (EC 2.7.8.5, phosphatidylglycerophosphate synthase) from Escherichia coli has been cloned, using pSC101 as the vector. The resulting hybrid plasmids not only correct the lack of in vitro synthase activity in pgsA strains but also cause an amplification (6- to 40-fold over wild-type levels) in enzymatic activity in direct proportion to the copy number of the plasmids found in vivo. The cloned gene also corrects the abnormally low level of polyglycerophosphatides found in pgsA strains and actually increases the level of phosphatidylglycerol to above that normally found in E. coli. The degree of alteration in phospholipid composition brought about by these hybrid plasmids is not of the order expected if fluctuations in enzyme levels in vivo were an important regulatory mechanism in phospholipid metabolism. The isolated hybrid plasmids have been mapped by restriction endonuclease analysis. The presence and location of other genetic markers have also been established. The above data, along with analysis of deletion derivatives of these plasmids and subcloning of appropriate restriction fragments, have established the position of the pgsA locus on the hybrid plasmids. From this data, the position of the pgsA locus has been determined to le between flaI and uvrC on the E. coli genetic map.
Collapse
|
21
|
Cloning of genes involved in membrane lipid synthesis. Effects of amplification of phosphatidylserine synthase in Escherichia coli. J Biol Chem 1981. [DOI: 10.1016/s0021-9258(19)69763-2] [Citation(s) in RCA: 58] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
|