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Article ; Online: Bacterial AsmA-Like Proteins

Sujeet Kumar / Natividad Ruiz

Contact, Vol

Bridging the Gap in Intermembrane Phospholipid Transport

2023 Volume 6

Abstract: In eukaryotic cells, nonvesicular lipid transport between organelles is mediated by lipid-transfer proteins. Recently, a new class of these lipid transporters has been described to facilitate the bulk of inter-organelle lipid transport at contact sites ... ...

Abstract	In eukaryotic cells, nonvesicular lipid transport between organelles is mediated by lipid-transfer proteins. Recently, a new class of these lipid transporters has been described to facilitate the bulk of inter-organelle lipid transport at contact sites by forming bridge-like structures with a hydrophobic groove through which lipids travel. Because their predicted structure is composed of repeating β-groove (RBG) domains, they have been named the RBG protein superfamily. Early studies on RBG proteins VPS13 and ATG2 recognized the resemblance of their predicted structures to that of the bacterial Lpt system, which transports newly synthesized lipopolysaccharides (LPS) between the inner and the outer membranes (IMs and OMs) of Gram-negative bacteria. In these didermic bacteria, the IMs and OMs are separated by an aqueous periplasmic compartment that is traversed by a bridge-like structure built with β-jelly roll domains from several Lpt proteins that provides a hydrophobic groove for LPS molecules to travel across the periplasm. Despite structural and functional similarities between RBG proteins and the Lpt system, the bacterial AsmA-like protein family has recently emerged as the likely ancestor of RBG proteins and long sought-after transporters that facilitate the transfer of phospholipids from the IM to the OM. Here, we review our current understanding of the structure and function of bacterial AsmA-like proteins, mainly focusing on recent studies that have led to the proposal that AsmA-like proteins mediate the bulk of phospholipid transfer between the IMs and OMs.
Keywords	Biology (General) ; QH301-705.5 ; Biochemistry ; QD415-436
Subject code	612
Language	English
Publishing date	2023-07-01T00:00:00Z
Publisher	SAGE Publishing
Document type	Article ; Online
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Article ; Online: Bacterial AsmA-Like Proteins: Bridging the Gap in Intermembrane Phospholipid Transport.

Kumar, Sujeet / Ruiz, Natividad

Contact (Thousand Oaks (Ventura County, Calif.))

2023 Volume 6, Page(s) 25152564231185931

Abstract	In eukaryotic cells, nonvesicular lipid transport between organelles is mediated by lipid-transfer proteins. Recently, a new class of these lipid transporters has been described to facilitate the bulk of inter-organelle lipid transport at contact sites by forming bridge-like structures with a hydrophobic groove through which lipids travel. Because their predicted structure is composed of repeating β-groove (RBG) domains, they have been named the RBG protein superfamily. Early studies on RBG proteins VPS13 and ATG2 recognized the resemblance of their predicted structures to that of the bacterial Lpt system, which transports newly synthesized lipopolysaccharides (LPS) between the inner and the outer membranes (IMs and OMs) of Gram-negative bacteria. In these didermic bacteria, the IMs and OMs are separated by an aqueous periplasmic compartment that is traversed by a bridge-like structure built with β-jelly roll domains from several Lpt proteins that provides a hydrophobic groove for LPS molecules to travel across the periplasm. Despite structural and functional similarities between RBG proteins and the Lpt system, the bacterial AsmA-like protein family has recently emerged as the likely ancestor of RBG proteins and long sought-after transporters that facilitate the transfer of phospholipids from the IM to the OM. Here, we review our current understanding of the structure and function of bacterial AsmA-like proteins, mainly focusing on recent studies that have led to the proposal that AsmA-like proteins mediate the bulk of phospholipid transfer between the IMs and OMs.
Language	English
Publishing date	2023-07-12
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	2964312-0
ISSN	2515-2564 ; 2515-2564
ISSN (online)	2515-2564
ISSN	2515-2564
DOI	10.1177/25152564231185931
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Article ; Online: The transmembrane α-helix of LptC participates in LPS extraction by the LptB

Wilson, Andrew / Ruiz, Natividad

Molecular microbiology

2022 Volume 118, Issue 1-2, Page(s) 61–76

Abstract: Lipopolysaccharide (LPS) is an essential component of the outer membrane of most Gram-negative bacteria that provides resistance to various toxic compounds and antibiotics. Newly synthesized LPS is extracted from the inner membrane by the ATP-binding ... ...

Abstract	Lipopolysaccharide (LPS) is an essential component of the outer membrane of most Gram-negative bacteria that provides resistance to various toxic compounds and antibiotics. Newly synthesized LPS is extracted from the inner membrane by the ATP-binding cassette (ABC) transporter LptB
MeSH term(s)	ATP-Binding Cassette Transporters/metabolism ; Adenosine Triphosphatases/metabolism ; Biological Transport ; Escherichia coli/genetics ; Escherichia coli/metabolism ; Escherichia coli Proteins/metabolism ; Lipopolysaccharides/metabolism ; Membrane Proteins/genetics ; Membrane Proteins/metabolism ; Protein Conformation, alpha-Helical
Chemical Substances	ATP-Binding Cassette Transporters ; Escherichia coli Proteins ; Lipopolysaccharides ; LptB protein, E coli ; LptC protein, E coli ; Membrane Proteins ; Adenosine Triphosphatases (EC 3.6.1.-)
Language	English
Publishing date	2022-06-27
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	619315-8
ISSN	1365-2958 ; 0950-382X
ISSN (online)	1365-2958
ISSN	0950-382X
DOI	10.1111/mmi.14952
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Article ; Online: How Escherichia coli Became the Flagship Bacterium of Molecular Biology.

Ruiz, Natividad / Silhavy, Thomas J

Journal of bacteriology

2022 Volume 204, Issue 9, Page(s) e0023022

Abstract: Escherichia coli is likely the most studied organism and was instrumental in developing many fundamental concepts in biology. But why E. coli? In the 1940s, E. coli was well suited for the biochemical and genetic research that blended to become the ... ...

Abstract	Escherichia coli is likely the most studied organism and was instrumental in developing many fundamental concepts in biology. But why E. coli? In the 1940s, E. coli was well suited for the biochemical and genetic research that blended to become the seminal field of biochemical genetics and led to the realization that processes already known to occur in complex organisms were conserved in bacteria. This now-obvious concept, combined with the advantages offered by its easy cultivation, ultimately drove many researchers to shift from the complexity of eukaryotic models to the simpler bacterial system, which eventually led to the development of molecular biology. As knowledge and experimental tools amassed, a positive-feedback loop fixed the central role of E. coli in research. However, given the vast diversity among bacteria and even among E. coli strains, it was by many fortuitous events that E. coli rose to the top as an experimental model. Here, we share how serendipity and its own biology selected E. coli as the flagship bacterium of molecular biology.
MeSH term(s)	Bacteria ; Escherichia coli/genetics ; Escherichia coli Infections ; Eukaryota ; Humans ; Molecular Biology
Language	English
Publishing date	2022-08-02
Publishing country	United States
Document type	Journal Article ; Review ; Research Support, N.I.H., Extramural
ZDB-ID	2968-3
ISSN	1098-5530 ; 0021-9193
ISSN (online)	1098-5530
ISSN	0021-9193
DOI	10.1128/jb.00230-22
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Article ; Online: Lipid Flippases for Bacterial Peptidoglycan Biosynthesis

Natividad Ruiz

Lipid Insights, Vol 2015, Iss Suppl. 1, Pp 21-

2016 Volume 31

Keywords	Science ; Q ; Chemistry ; QD1-999 ; Organic chemistry ; QD241-441
Publishing date	2016-01-01T00:00:00Z
Publisher	Libertas Academica
Document type	Article ; Online
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Article ; Online: Transport of lipopolysaccharides and phospholipids to the outer membrane.

Wilson, Andrew / Ruiz, Natividad

Current opinion in microbiology

2021 Volume 60, Page(s) 51–57

Abstract: Cells must build and maintain at least one membrane that surrounds essential cellular components and provides structural integrity. Gram-negative bacteria possess an inner membrane, which separates the aqueous cytoplasmic and periplasmic compartments, ... ...

Abstract	Cells must build and maintain at least one membrane that surrounds essential cellular components and provides structural integrity. Gram-negative bacteria possess an inner membrane, which separates the aqueous cytoplasmic and periplasmic compartments, and an outer membrane, which surrounds the periplasm. The outer membrane is an asymmetric bilayer with phospholipids in its inner leaflet and lipopolysaccharides in its outer leaflet. This structure provides cellular integrity and prevents the entry of many toxic compounds into the cell. Constructing the outer membrane is challenging, since its lipid constituents must be synthesized within the inner membrane, transported across the periplasm, and ultimately assembled into an asymmetric structure. This review highlights major recent advances in our understanding of the mechanism and structure of the intermembrane, multi-protein machine that transports lipopolysaccharide across the cell envelope. Although our understanding of phospholipid transport is very limited, we also provide a brief update on this topic.
MeSH term(s)	Bacterial Outer Membrane Proteins/metabolism ; Biological Transport ; Cell Membrane/metabolism ; Escherichia coli Proteins/metabolism ; Gram-Negative Bacteria/metabolism ; Lipopolysaccharides/metabolism ; Phospholipids/metabolism
Chemical Substances	Bacterial Outer Membrane Proteins ; Escherichia coli Proteins ; Lipopolysaccharides ; Phospholipids
Language	English
Publishing date	2021-02-15
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Review
ZDB-ID	1418474-6
ISSN	1879-0364 ; 1369-5274
ISSN (online)	1879-0364
ISSN	1369-5274
DOI	10.1016/j.mib.2021.01.006
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Article: Lipid Flippases for Bacterial Peptidoglycan Biosynthesis.

Ruiz, Natividad

Lipid insights

2016 Volume 8, Issue Suppl 1, Page(s) 21–31

Abstract: The biosynthesis of cellular polysaccharides and glycoconjugates often involves lipid-linked intermediates that need to be translocated across membranes. Essential pathways such as N-glycosylation in eukaryotes and biogenesis of the peptidoglycan (PG) ... ...

Abstract	The biosynthesis of cellular polysaccharides and glycoconjugates often involves lipid-linked intermediates that need to be translocated across membranes. Essential pathways such as N-glycosylation in eukaryotes and biogenesis of the peptidoglycan (PG) cell wall in bacteria share a common strategy where nucleotide-sugars are used to build a membrane-bound oligosaccharide precursor that is linked to a phosphorylated isoprenoid lipid. Once made, these lipid-linked intermediates must be translocated across a membrane so that they can serve as substrates in a different cellular compartment. How translocation occurs is poorly understood, although it clearly requires a transporter or flippase. Identification of these transporters is notoriously difficult, and, in particular, the identity of the flippase of lipid II, an intermediate required for PG biogenesis, has been the subject of much debate. Here, I will review the body of work that has recently fueled this controversy, centered on proposed flippase candidates FtsW, MurJ, and AmJ.
Language	English
Publishing date	2016-01-13
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	2455275-6
ISSN	1178-6353
ISSN	1178-6353
DOI	10.4137/LPI.S31783
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Article ; Online: Filling holes in peptidoglycan biogenesis of Escherichia coli.

Ruiz, Natividad

Current opinion in microbiology

2016 Volume 34, Page(s) 1–6

Abstract: The peptidoglycan cell wall is an essential mesh-like structure in most bacteria. It is built outside the cytoplasmic membrane by polymerizing a disaccharide-pentapeptide into glycan chains that are crosslinked by peptides. The disaccharide-pentapeptide ... ...

Abstract	The peptidoglycan cell wall is an essential mesh-like structure in most bacteria. It is built outside the cytoplasmic membrane by polymerizing a disaccharide-pentapeptide into glycan chains that are crosslinked by peptides. The disaccharide-pentapeptide is synthetized as a lipid-linked precursor called lipid II, which is exported across the cytoplasmic membrane so that synthases can make new glycan chains. Growth of the peptidoglycan wall requires careful balancing of synthesis of glycan chains and hydrolysis of the preexisting structure to allow incorporation of new material. Recent studies in Escherichia coli have advanced our understanding of lipid II translocation across the membrane and how synthases are regulated to ensure proper envelope growth.
MeSH term(s)	Cell Membrane/metabolism ; Cell Wall/metabolism ; Escherichia coli/metabolism ; Escherichia coli Proteins/metabolism ; Peptidoglycan/metabolism ; Polysaccharides/metabolism
Chemical Substances	Escherichia coli Proteins ; Peptidoglycan ; Polysaccharides
Language	English
Publishing date	2016-07-22
Publishing country	England
Document type	Journal Article ; Review ; Research Support, N.I.H., Extramural
ZDB-ID	1418474-6
ISSN	1879-0364 ; 1369-5274
ISSN (online)	1879-0364
ISSN	1369-5274
DOI	10.1016/j.mib.2016.07.010
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Article ; Online: Use of Mutagenesis and Functional Screens to Characterize Essential Genes Involved in Lipopolysaccharide Transport.

Wilson, Andrew / Iniguez, Carlos / Ruiz, Natividad

Methods in molecular biology (Clifton, N.J.)

2022 Volume 2548, Page(s) 3–19

Abstract: Structure-function analysis is a powerful strategy to characterize the contribution of specific residues to the biogenesis and function of a protein. This approach requires the characterization of strains that express mutant alleles in the absence of the ...

Abstract	Structure-function analysis is a powerful strategy to characterize the contribution of specific residues to the biogenesis and function of a protein. This approach requires the characterization of strains that express mutant alleles in the absence of the wild-type protein. When studying nonessential bacterial genes, collections of mutants can be easily constructed by introducing plasmid-encoded alleles of interest into a strain that already lacks the wild-type gene. However, this high-throughput approach is not applicable to studying essential genes since their respective null strains are not viable. While there are several tools currently available to modify essential genes, they can be greatly limited by the amount of effort it takes to build and analyze each mutant strain. Here, we describe a high-throughput system for the rapid structure-function analysis of essential genes involved in lipopolysaccharide transport in Escherichia coli. This method, which can be applied to study any essential gene, relies on the initial construction of a single bacterial strain that can be used to generate and functionally characterize multiple plasmid-encoded alleles in under 24 h. We will discuss the advantages and possible shortcomings of our protocol in comparison to other commonly used methods.
MeSH term(s)	Escherichia coli/genetics ; Escherichia coli/metabolism ; Genes, Bacterial ; Genes, Essential ; Lipopolysaccharides/metabolism ; Mutagenesis ; Plasmids/genetics
Chemical Substances	Lipopolysaccharides
Language	English
Publishing date	2022-09-23
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-2581-1_1
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Article ; Online: The Bacterial Cell Wall: From Lipid II Flipping to Polymerization.

Kumar, Sujeet / Mollo, Aurelio / Kahne, Daniel / Ruiz, Natividad

Chemical reviews

2022 Volume 122, Issue 9, Page(s) 8884–8910

Abstract: The peptidoglycan (PG) cell wall is an extra-cytoplasmic glycopeptide polymeric structure that protects bacteria from osmotic lysis and determines cellular shape. Since the cell wall surrounds the cytoplasmic membrane, bacteria must add new material to ... ...

Abstract	The peptidoglycan (PG) cell wall is an extra-cytoplasmic glycopeptide polymeric structure that protects bacteria from osmotic lysis and determines cellular shape. Since the cell wall surrounds the cytoplasmic membrane, bacteria must add new material to the PG matrix during cell elongation and division. The lipid-linked precursor for PG biogenesis, Lipid II, is synthesized in the inner leaflet of the cytoplasmic membrane and is subsequently translocated across the bilayer so that the PG building block can be polymerized and cross-linked by complex multiprotein machines. This review focuses on major discoveries that have significantly changed our understanding of PG biogenesis in the past decade. In particular, we highlight progress made toward understanding the translocation of Lipid II across the cytoplasmic membrane by the MurJ flippase, as well as the recent discovery of a novel class of PG polymerases, the SEDS (shape, elongation, division, and sporulation) glycosyltransferases RodA and FtsW. Since PG biogenesis is an effective target of antibiotics, these recent developments may lead to the discovery of much-needed new classes of antibiotics to fight bacterial resistance.
MeSH term(s)	Anti-Bacterial Agents/metabolism ; Bacteria/metabolism ; Bacterial Proteins/metabolism ; Cell Wall/metabolism ; Peptidoglycan/chemistry ; Peptidoglycan/metabolism ; Polymerization ; Uridine Diphosphate N-Acetylmuramic Acid/analogs & derivatives
Chemical Substances	Anti-Bacterial Agents ; Bacterial Proteins ; Peptidoglycan ; Uridine Diphosphate N-Acetylmuramic Acid ; muramyl-NAc-(pentapeptide)pyrophosphoryl-undecaprenol
Language	English
Publishing date	2022-03-11
Publishing country	United States
Document type	Journal Article ; Review ; Research Support, N.I.H., Extramural
ZDB-ID	207949-5
ISSN	1520-6890 ; 0009-2665
ISSN (online)	1520-6890
ISSN	0009-2665
DOI	10.1021/acs.chemrev.1c00773
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