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6S RNA Function Enhances Long-Term Cell Survival. Amy E. Trotochaud, 2004.6S RNA was identified in Escherichia coli >30 years ago, but the physiological role of this RNA has remained elusive . Here, we demonstrate that 6S RNA-deficient cells are at a disadvantage for survival in stationary phase, a time when 6S RNA regulates transcription . Growth defects were most apparent as a decrease in the competitive fitness of cells lacking 6S RNA . To decipher the molecular mechanisms underlying the growth defects, we have expanded studies of 6S RNA effects on transcription . 6S RNA inhibition of  70-dependent
transcription was not ubiquitous, in spite of the fact that the vast
majority of
70-RNA
polymerase is bound by 6S RNA during stationary phase . The
70-dependent
promoters inhibited by 6S RNA contain an extended –10 promoter
element, suggesting that this feature may define a class of 6S
RNA-regulated genes . We also discovered a secondary effect of 6S RNA
in the activation of
S-dependent
transcription at several promoters . We conclude that 6S RNA
regulation of both
70
and
S
activities contributes to increased cell persistence during nutrient
deprivation .
Diversity of Tn4001 Transposition Products: the Flanking IS256 Elements Can Form Tandem Dimers and IS Circles. M. Prudhomme, 2002.We show that both flanking IS256 elements carried by transposon Tn4001 are capable of generating head-to-tail tandem copies and free circular forms, implying that both are active . Our results suggest that the tandem structures arise from dimeric copies of the donor or vector plasmid present in the population by a mechanism in which an IS256 belonging to one Tn4001 copy attacks an IS256 end carried by the second Tn4001 copy . The resulting structures carry abutted left (inverted left repeat [IRL]) and right (inverted right repeat [IRR]) IS256 ends . Examination of the junction sequence suggested that it may form a relatively good promoter capable of driving transposase synthesis in Escherichia coli . This behavior resembles that of an increasing number of bacterial insertion sequences which generate integrative junctions as part of the transposition cycle . Sequence analysis of the IRL-IRR junctions demonstrated that attack of one end by the other is largely oriented (IRL attacks IRR) . Our experiments also defined the functional tips of IS256 as the tips predicted from sequence alignments, confirming that the terminal 4 bp at each end are indeed different . The appearance of these multiple plasmid and transposon forms indicates that care should be exercised when Tn4001 is used in transposition mutagenesis . This is especially true when it is used with naturally transformable hosts, such as Streptococcus pneumoniae, in which reconstitution of the donor plasmid may select for higher-order multimers . Heterocyst-Specific Expression of patB, a Gene Required for Nitrogen Fixation in Anabaena sp . Strain PCC 7120. Kathryn M. Jones, 2003.The patB gene product is required for growth and survival of the filamentous cyanobacterium Anabaena sp . strain PCC 7120 in the absence of combined nitrogen . A patB::gfp fusion demonstrated that this gene is expressed exclusively in heterocysts . patB mutants have a normal initial pattern of heterocyst spacing along the filament but differentiate excess heterocysts after several days in the absence of combined nitrogen . Expression of hetR and patS, two critical regulators of the heterocyst development cascade, are normal for patB mutants, indicating that patB acts downstream of them in the differentiation pathway . A patB deletion mutant suffers an almost complete cessation of growth and nitrogen fixation within 24 h of combined nitrogen removal . In contrast, a new PatB mutant that is defective in its N-terminal ferredoxin domain, or a previously described mutant that has a frameshift removing its C-terminal helix-turn-helix domain, grows very slowly and differentiates multiple contiguous heterocysts under nitrogen-deficient conditions .
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