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AmtB Is Necessary for NH4+-Induced Nitrogenase Switch-Off and ADP-Ribosylation in Rhodobacter capsulatus. Alexander F. Yakunin, 2002.Rhodobacter capsulatus possesses two genes potentially coding for ammonia transporters, amtB and amtY . In order to better understand their role in the physiology of this bacterium and their possible significance in nitrogen fixation, we created single-knockout mutants . Strains mutated in either amtB or amtY did not show a growth defect under any condition tested and were still capable of taking up ammonia at nearly wild-type rates, but an amtB mutant was no longer capable of transporting methylamine . The amtB strain but not the amtY strain was also totally defective in carrying out ADP-ribosylation of Fe-protein or the switch-off of in vivo nitrogenase activity in response to NH4+ addition . ADP-ribosylation in response to darkness was unaffected in amtB and amtBY strains, and glutamine synthetase activity was normally regulated in these strains in response to ammonium addition, suggesting that one role of AmtB is to function as an ammonia sensor for the processes that regulate nitrogenase activity . immX Immunity Region of Rhizobium Phage 16-3: Two Overlapping Cistrons of Repressor Function. Zsolt Csiszovszki, 2003.16-3 is a temperate phage of the symbiotic nitrogen-fixing bacterium Rhizobium meliloti 41 . Its prophage state and immunity against superinfection by homoimmune phages are governed by a complex set of controls: the immC and immX repressor systems and the avirT element are all located in well-separated, distinct regions which span 25 kb on the bacteriophage chromosome . The anatomy and function of the immC region are well documented; however, fewer analyses have addressed the immX and avirT regions . We focused in this paper on the immX region and dissected it into two major parts: XU/L and XV . The XU/L part (0.6 kb) contained two overlapping cistrons, XU and XL, coding for proteins pXU and pXL, respectively . Inactivation of either gene inactivated the repressor function of the immX region . Loss-of-function mutants of XU and XL complemented each other in trans in double lysogens . The XV part (1 kb) contained a target for XU/L repressor action . Mutations at three sites in XV led to various degree of ImmX insensitivity in a hierarchic manner . Two sites (XV1 and XV3) exhibited the inverted-repeat structures characteristic of many repressor binding sites . However, XV1 could also be folded into a transcription terminator . Of the two immunity regions of 16-3, immX seems to be unique both in its complex genetic anatomy and in its sequence . To date, no DNA or peptide sequence homologous to that of ImmX has been found in the data banks . In contrast, immC shares properties of a number of immunity systems commonly found in temperate phages . Isolation of a Methanogen from Deep Marine Sediments That Contain Methane Hydrates, and Description of Methanoculleus submarinus sp . nov.. Jill A. Mikucki, 2003.We isolated a methanogen from deep in the sediments of the Nankai Trough off the eastern coast of Japan . At the sampling site, the water was 950 m deep and the sediment core was collected at 247 m below the sediment surface . The isolated methanogen was named Nankai-1 . Cells of Nankai-1 were nonmotile and highly irregular coccoids (average diameter, 0.8 to 2 µm) and grew with hydrogen or formate as a catabolic substrate . Cells required acetate as a carbon source . Yeast extract and peptones were not required but increased the growth rate . The cells were mesophilic, growing most rapidly at 45°C (no growth at  10°C or
 55°C) . Cells grew with a maximum specific growth rate of 2.43 day-1 at 45°C . Cells grew at pH values between 5.0 and 8.7 but did not grow at pH 4.7 or 9.0 . Strain Nankai-1 grew in a wide range of salinities, from 0.1 to 1.5 M Na+ . The described phenotypic characteristics of this novel isolate were consistent with the in situ environment of the Nankai Trough . This is the first report of a methanogenic isolate from methane hydrate-bearing sediments . Phylogenetic analysis of its 16S rRNA gene sequence indicated that it is most closely related to Methanoculleus marisnigri (99.1% sequence similarity), but DNA hybridization experiments indicated a DNA sequence similarity of only 49% . Strain Nankai-1 was also found to be phenotypically similar to M . marisnigri, but two major phenotypic differences were found: strain Nankai-1 does not require peptones, and it grows fastest at a much higher temperature . We propose a new species, Methanoculleus submarinus, with strain Nankai-1 as the type strain .
Characterization of Multiple-Substrate Utilization by Anthracene-Degrading Mycobacterium frederiksbergense LB501T. Lukas Y. Wick, 2003.Stable carbon isotope analysis of biomass and analyses of phospholipid fatty acids (PLFA), glycolipid fatty acids (GLFA), and mycolic acids were used to characterize mixed-substrate utilization by Mycobacterium frederiksbergense LB501T under various substrate regimens . The distinct 13C contents of anthracene and glucose as representatives of typical hydrophobic pollutants and naturally occurring organic compounds, respectively, were monitored during formation into biomass and used to quantify the relative contributions of the two carbon sources to biomass formation . Moreover, the influence of mixed-substrate utilization on PLFA, GLFA, and mycolic acid profiles and cell surface hydrophobicity was investigated . Results revealed that M . frederiksbergense LB501T degrades anthracene and forms biomass from it even in the presence of more readily available dissolved glucose . The relative ratios of straight-chain saturated PLFA to the corresponding unsaturated PLFA and the total fraction of saturated cyclopropyl-branched PLFA of M . frederiksbergense LB501T depended on the carbon source and the various rates of addition of mixed substrates, whereas no such trend was observed with GLFA . Higher proportions of anthracene in the carbon source mixture led to higher cell surface hydrophobicities and more-hydrophobic mycolic acids, which in turn appeared to be valuable indicators for substrate utilization by M . frederiksbergense LB501T . The capability of polycyclic aromatic hydrocarbon (PAH)-degrading bacteria to utilize readily available substrates besides the poorly available PAHs favors the buildup of PAH-degrading biomass . Feeding of supplementary carbon substrates may therefore promote bioremediation, provided that it sustains the pollutant-degrading population rather than other members of the microbial community .
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