Salt‐dependent regulation of archaellins in
            Haloarcula marismortui

ABSTRACT Microbial rhodopsins, a diverse group of photoactive proteins found in Archaea, Bacteria, and Eukarya, function in photosensing and photoenergy harvesting and may have been present in the resource-limited early global environment. Four different physiological functions have been identified and characterized for nearly 5,000 retinal-binding photoreceptors, these being ion transporters that transport proton or chloride and sensory rhodopsins that mediate light-attractant and/or -repellent responses. The greatest number of rhodopsins previously observed in a single archaeon had been four. Here, we report a newly discovered six-rhodopsin system in a single archaeon, Haloarcula marismortui, which shows a more diverse absorbance spectral distribution than any previously known rhodopsin system, and, for the first time, two light-driven proton transporters that respond to the same wavelength. All six rhodopsins, the greatest number ever identified in a single archaeon, were first shown to be expressed in H. marismortui, and these were then overexpressed in Escherichia coli. The proteins were purified for absorption spectra and photocycle determination, followed by measurement of ion transportation and phototaxis. The results clearly indicate the existence of a proton transporter system with two isochromatic rhodopsins and a new type of sensory rhodopsin-like transducer in H. marismortui.

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Negamycin Binds to the Wall of the Nascent Chain Exit Tunnel of the 50S Ribosomal Subunit

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00455-07 ◽

2007 ◽

Vol 51 (12) ◽

pp. 4462-4465 ◽

Cited By ~ 27

Author(s):

Susan J. Schroeder ◽

Gregor Blaha ◽

Peter B. Moore

Keyword(s):

Protein Synthesis ◽

Small Molecule ◽

Ribosomal Subunit ◽

Small Molecule Inhibitor ◽

Single Site ◽

Haloarcula Marismortui ◽

Molecule Inhibitor ◽

Nascent Chain ◽

Exit Tunnel ◽

Inhibitor Of Protein Synthesis

ABSTRACT Negamycin, a small-molecule inhibitor of protein synthesis, binds the Haloarcula marismortui 50S ribosomal subunit at a single site formed by highly conserved RNA nucleotides near the cytosolic end of the nascent chain exit tunnel. The mechanism of antibiotic action and the function of this unexplored tunnel region remain intriguingly elusive.

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Methylomes of Two Extremely Halophilic Archaea Species, Haloarcula marismortui and Haloferax mediterranei

Microbiology Resource Announcements ◽

10.1128/mra.00577-19 ◽

2019 ◽

Vol 8 (27) ◽

Cited By ~ 1

Author(s):

Shiladitya DasSarma ◽

Alexey Fomenkov ◽

Satyajit L. DasSarma ◽

Tamas Vincze ◽

Priya DasSarma ◽

...

Keyword(s):

Single Molecule ◽

Gene Annotation ◽

Halophilic Archaea ◽

Restriction Enzymes ◽

Haloferax Mediterranei ◽

Haloarcula Marismortui ◽

Content Type ◽

Extremely Halophilic Archaea ◽

Large Plasmids ◽

Methyl Cytosine

ABSTRACT The genomes of two extremely halophilic Archaea species, Haloarcula marismortui and Haloferax mediterranei, were sequenced using single-molecule real-time sequencing. The ∼4-Mbp genomes are GC rich with multiple large plasmids and two 4-methyl-cytosine patterns. Methyl transferases were incorporated into the Restriction Enzymes Database (REBASE), and gene annotation was incorporated into the Haloarchaeal Genomes Database (HaloWeb).

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RiboVision suite for visualization and analysis of ribosomes

Faraday Discussions ◽

10.1039/c3fd00126a ◽

2014 ◽

Vol 169 ◽

pp. 195-207 ◽

Cited By ~ 62

Author(s):

Chad R. Bernier ◽

Anton S. Petrov ◽

Chris C. Waterbury ◽

James Jett ◽

Fengbo Li ◽

...

Keyword(s):

Molecular Interactions ◽

Ribosomal Proteins ◽

Secondary Structures ◽

Macromolecular Complex ◽

Analysis Tool ◽

Complex Data ◽

Helical Structures ◽

Haloarcula Marismortui ◽

3D Structures ◽

2D And 3D

RiboVision is a visualization and analysis tool for the simultaneous display of multiple layers of diverse information on primary (1D), secondary (2D), and three-dimensional (3D) structures of ribosomes. The ribosome is a macromolecular complex containing ribosomal RNA and ribosomal proteins and is a key component of life responsible for the synthesis of proteins in all living organisms. RiboVision is intended for rapid retrieval, analysis, filtering, and display of a variety of ribosomal data. Preloaded information includes 1D, 2D, and 3D structures augmented by base-pairing, base-stacking, and other molecular interactions. RiboVision is preloaded with rRNA secondary structures, rRNA domains and helical structures, phylogeny, crystallographic thermal factors,etc.RiboVision contains structures of ribosomal proteins and a database of their molecular interactions with rRNA. RiboVision contains preloaded structures and data for two bacterial ribosomes (Thermus thermophilusandEscherichia coli), one archaeal ribosome (Haloarcula marismortui), and three eukaryotic ribosomes (Saccharomyces cerevisiae,Drosophila melanogaster, andHomo sapiens). RiboVision revealed several major discrepancies between the 2D and 3D structures of the rRNAs of the small and large subunits (SSU and LSU). Revised structures mapped with a variety of data are available in RiboVision as well as in a public gallery (http://apollo.chemistry.gatech.edu/RibosomeGallery). RiboVision is designed to allow users to distill complex data quickly and to easily generate publication-quality images of data mapped onto secondary structures. Users can readily import and analyze their own data in the context of other work. This package allows users to import and map data from CSV files directly onto 1D, 2D, and 3D levels of structure. RiboVision has features in rough analogy with web-based map services capable of seamlessly switching the type of data displayed and the resolution or magnification of the display. RiboVision is available at http://apollo.chemistry.gatech.edu/RiboVision.

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Detecting Protein-Protein Interactions in the Intact Cell of Bacillus subtilis (ATCC 6633)

Journal of Bacteriology ◽

10.1128/jb.185.14.4268-4275.2003 ◽

2003 ◽

Vol 185 (14) ◽

pp. 4268-4275 ◽

Cited By ~ 8

Author(s):

Michael S. Winters ◽

R. A. Day

Keyword(s):

Bacillus Subtilis ◽

Protein Interactions ◽

Ribosomal Proteins ◽

Intact Cell ◽

Protein Biosynthesis ◽

Polyacrylamide Gel Electrophoresis ◽

Protein Database ◽

Haloarcula Marismortui ◽

Associated Proteins ◽

Covalently Linked

ABSTRACT The salt bridge, paired group-specific reagent cyanogen (ethanedinitrile; C2N2) converts naturally occurring pairs of functional groups into covalently linked products. Cyanogen readily permeates cell walls and membranes. When the paired groups are shared between associated proteins, isolation of the covalently linked proteins allows their identity to be assigned. Examination of organisms of known genome sequence permits identification of the linked proteins by mass spectrometric techniques applied to peptides derived from them. The cyanogen-linked proteins were isolated by polyacrylamide gel electrophoresis. Digestion of the isolated proteins with proteases of known specificity afforded sets of peptides that could be analyzed by mass spectrometry. These data were compared with those derived theoretically from the Swiss Protein Database by computer-based comparisons (Protein Prospector; http://prospector.ucsf.edu ). Identification of associated proteins in the ribosome of Bacillus subtilis strain ATCC 6633 showed that there is an association homology with the association patterns of the ribosomal proteins of Haloarcula marismortui and Thermus thermophilus. In addition, other proteins involved in protein biosynthesis were shown to be associated with ribosomal proteins.

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