A plethora of non-coding RNAs has been discovered using high-resolution transcriptomics tools, indicating that transcriptional and post-transcriptional regulation is much more complex than previously appreciated. Small RNAs associated with transcription start sites of annotated coding regions (TSSaRNAs) are pervasive in both eukaryotes and bacteria. Here, we provide evidence for existence of TS...

Predicting protein interaction modules from a network of protein interactions is a challenging task. In this paper, we propose to use a clique finding algorithm to compute cliques and quasi-cliques in the network. We first derive a new algorithm based on the generalized Motzkin-Strauss Formalism. We then prove the correctness and convergence of the algorithm. The algorithm is extremely simple t...

A broad range of antibiotics affecting protein biosynthesis were screened for their ability to inhibit growth of the archaeon Halobacterium halobium. Only a few drugs, including chloramphenicol, produced inhibitory effects. Mutants which showed increased resistance to chloramphenicol were isolated; of the nine tested, eight exhibited a C----U transition at position 2471 and the ninth had an A--...

Malate dehydrogenase from the extreme halophile Halobacterium marismortui crystallizes in highly concentrated phosphate solution in space group 12 with cell dimensions a = 113.8 A, b = 122.8 A, c = 126.7 A, beta = 98.1 degrees. The halophilic enzyme was found to be unstable at lower concentrations of phosphate. It associates with unusually large amounts of water and salt, and the combined parti...

The obligate halophile, Halobacterium salinarium, maintains a rod-shaped morphology under normal growth conditions. Lactoperoxidase(EC 1.11.1.7;donor:hydrogen-peroxide oxidoreductase)-catalyzed iodination and treatment with proteolytic enzymes were used to demonstrate that the recently described envelope glycoprotein (Mescher, M.F. & Strominger, J.L. (1976) J. Biol. Chem. 251, 2005-2014) is the...

This review deals with the role of carboxylic amino acids in the proton transport activity of bacteriorhodopsin. The main focus is on the infrared data, which allow direct monitoring of the protonation/deprotonation of specific residues dur ing the proton movement in the course of the photocycle. Additional attention is paid to the potential use of carboxylic acids in proteins as internal senso...

Previous work demonstrated that the TrmB transcription factor is responsible for regulating the expression of many enzyme-coding genes in the hypersaline-adapted archaeon Halobacterium salinarum via a direct interaction with a cis-regulatory sequence in their promoters. This interaction is abolished in the presence of glucose. Although much is known about the effects of TrmB at the transcriptio...