Genomic and genetic dissection of an archaeal regulon
Nitin S. Baliga,Nitin S. Baliga,Sean Kennedy,Wailap Victor Ng,Leroy Hood,Shiladitya DasSarma +5 more
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TLDR
Similarities of the bop-like UAS and transcription factors in diverse organisms, including a plant and a γ-proteobacterium, suggest an ancient origin for this regulon capable of coordinating light and oxygen responses in the three major branches of the evolutionary tree of life.Abstract:
The extremely halophilic archaeon Halobacterium sp. NRC-1 can grow phototrophically by means of light-driven proton pumping by bacteriorhodopsin in the purple membrane. Here, we show by genetic analysis of the wild type, and insertion and double-frame shift mutants of Bat that this transcriptional regulator coordinates synthesis of a structural protein and a chromophore for purple membrane biogenesis in response to both light and oxygen. Analysis of the complete Halobacterium sp. NRC-1 genome sequence showed that the regulatory site, upstream activator sequence (UAS), the putative binding site for Bat upstream of the bacterio-opsin gene (bop), is also present upstream to the other Bat-regulated genes. The transcription regulator Bat contains a photoresponsive cGMP-binding (GAF) domain, and a bacterial AraC type helix–turn–helix DNA binding motif. We also provide evidence for involvement of the PAS/PAC domain of Bat in redox-sensing activity by genetic analysis of a purple membrane overproducer. Five additional Bat-like putative regulatory genes were found, which together are likely to be responsible for orchestrating the complex response of this archaeon to light and oxygen. Similarities of the bop-like UAS and transcription factors in diverse organisms, including a plant and a γ-proteobacterium, suggest an ancient origin for this regulon capable of coordinating light and oxygen responses in the three major branches of the evolutionary tree of life. Finally, sensitivity of four of five regulon genes to DNA supercoiling is demonstrated and correlated to presence of alternating purine–pyrimidine sequences (RY boxes) near the regulated promoters.read more
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References
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Journal ArticleDOI
Bacterial Rhodopsin: Evidence for a New Type of Phototrophy in the Sea
Oded Béjà,L. Aravind,Eugene V. Koonin,Marcelino T. Suzuki,Andrew G. Hadd,Linh Nguyen,Stevan B. Jovanovich,Christian M. Gates,Robert A. Feldman,John L. Spudich,Elena N. Spudich,Edward F. DeLong +11 more
TL;DR: The results demonstrate that archaeal-like rhodopsins are broadly distributed among different taxa, including members of the domain Bacteria, and indicate that a previously unsuspected mode of bacterially mediated light-driven energy generation may commonly occur in oceanic surface waters worldwide.
Journal ArticleDOI
Functions of a New Photoreceptor Membrane
TL;DR: Preliminary results indicate that the gradient in H. halobium plays the central role in energy coupling attributed to such electrochemical gradients by Mitchell's chemiosmotic theory.
Journal ArticleDOI
Genome sequence of Halobacterium species NRC-1
Wailap Victor Ng,Wailap Victor Ng,Sean Kennedy,Gregory G. Mahairas,Gregory G. Mahairas,Brian R. Berquist,Min Pan,Min Pan,Hem D. Shukla,Stephen R. Lasky,Stephen R. Lasky,Nitin S. Baliga,Vesteinn Thorsson,Vesteinn Thorsson,Jennifer L. Sbrogna,Steven Swartzell,Douglas Weir,John A. Hall,Timothy A. Dahl,Timothy A. Dahl,Russell Welti,Russell Welti,Young Ah Goo,Young Ah Goo,Brent Leithauser,Kim Keller,Randy Cruz,Michael J. Danson,David W. Hough,Deborah G. Maddocks,Peter E. Jablonski,Mark P. Krebs,Christine M. Angevine,Heather Dale,Thomas A. Isenbarger,Ronald F. Peck,Mechthild Pohlschroder,John L. Spudich,Kwang Hwan Jung,Maqsudul Alam,Tracey Allen K. Freitas,Shaobin Hou,Charles J. Daniels,Patrick P. Dennis,Arina D. Omer,Holger Ebhardt,Todd M. Lowe,Ping Liang,Monica Riley,Leroy Hood,Leroy Hood,Shiladitya DasSarma +51 more
TL;DR: Analysis of the genome sequence shows the presence of pathways for uptake and utilization of amino acids, active sodium-proton antiporter and potassium uptake systems, sophisticated photosensory and signal transduction pathways, and DNA replication, transcription, and translation systems resembling more complex eukaryotic organisms.
Journal ArticleDOI
Direct Targeting of Light Signals to a Promoter Element-Bound Transcription Factor
TL;DR: It is suggested that the phytochromes may function as integral light-switchable components of transcriptional regulator complexes, permitting continuous and immediate sensing of changes in this environmental signal directly at target gene promoters.
Journal ArticleDOI
Retinylidene Proteins: Structures and Functions from Archaea to Humans
TL;DR: The aims of this review are to examine this group of photoactive proteins as a whole, to summarize the current understanding of structure/function relationships in the best-studied examples, and to report recent new developments.
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