Summary: The genetic organization of the left edge (tylEDHFJ region) of the tylosin biosynthetic gene cluster from Streptomyces fradiae has been determined. Sequence analysis of a 12·9 kb region has revealed the presence of 11 ORFs, 10 of them belonging to the biosynthetic cluster. The putative functions of the proteins encoded by these genes are as follows: peptidase (ORF1, ddcA), tylosin resistance determinant (ORF2, tlrB), glycosyltransferase (ORF3, tylN), methyltransferase (ORF4, tylE), ketoreductase (ORF5, tylD), ferredoxin (ORF6, tylH2), cytochrome P450 (ORF7, tylH1), methyltransferase (ORF8, tylF), epimerase (ORF9, tylJ), acyl-CoA oxidase (ORF10, tylP) and receptor of regulatory factors (ORF11, tylQ). The functional identification of the genes in the proposed tylosin biosynthetic pathway has been deduced by database searches and previous genetic complementation studies performed with tylosin idiotrophic mutants blocked at various stages in tylosin biosynthesis. The tlrB gene has been shown to be useful as a tylosin resistance marker in Streptomyces lividans, Streptomyces parvulus and Streptomyces coelicolor and the effect of tylF on macrocin depletion has been confirmed. A pathway for the biosynthesis of 6-deoxy-D-allose, the unmethylated mycinose precursor, involving the genes tylD, tylJ and tylN is proposed.
Summary: Bacillus subtilis responds to various stimuli (heat, ethanol and salt stress, energy starvation) with the induction of general stress proteins (GSPs). Most of them belong to the stress and stationary-phase regulon controlled by the alternative sigma factor σB. The majority of σB-dependent proteins are thought to provide a precautionary general stress resistance in stressed or starved cells. In this report, the identification and transcriptional analysis of nine new members of the σB regulon are described. The biochemical function was not determined for any of the proteins encoded by the nine new σB-dependent stress genes, however, similarities to proteins in the databases allowed a distinction between proteins with putative (i-iv) and unknown (v) function. The putative functions of BmrU, YcdF, YdaD, YdaP, YhdN and YocK underline the suggested protective role of σB-dependent GSPs and also elucidate new areas where σB might play an important role. (i) The finding that the bmrUR operon is under σB control indicates that the elimination of multidrug compounds might be a new function in multiple stress resistance. (ii) YcdF and YdaD resemble NAD(P)-dependent dehydrogenases. Both proteins could be involved in the generation of NAD(P)H and therefore in the maintenance of the intracellular redox balance under stress. (iii) The ydaP gene might belong to the increasing number of σB-dependent genes whose orthologues are under the control of σS in Escherichia coli, indicating that both regulons may fulfil similar functions. (iv) YhdN shows weak similarities to potassium ion channel proteins and YocK shows resemblance to the DnaK suppressor protein DksA. (v) Three new σB-dependent genes (ydaE, ydaG and yfkM) encoding proteins with still unknown functions were also described. Further analyses of corresponding mutants might allow a first prediction of their function within the framework of the general stress regulon.
Summary: The genome sequence of Mycobacterium tuberculosis H37Rv was found to contain 56 loci with homology to insertion sequences (ISs). As well as the previously described IS6110, IS1081, IS1547 and IS-like elements, new ISs belonging to the IS3, IS5, IS21, IS30, IS110, IS256 and ISL3 families were identified. In addition, six ISs created a grouping of their own to form a new family (the IS1535 family). Elements with similarity to ISs in other actinomycetes were identified, suggesting the movement of ISs between related genera. The location of ISs on the chromosome revealed that an approximately 600 kb region close to the origin of replication lacks ISs, pointing to the possible detrimental effect of insertions in this area. Analysis of the distribution of ISs through the tubercle strains Mycobacterium africanum, M. microti, M. bovis, M. bovis BCG Pasteur, M. tuberculosis H37Ra, M. tuberculosis CSU#93 and 29 clinical isolates revealed that only IS1532, IS1533, IS1534, and IS1561 were absent from some of the strains tested. A novel repeated sequence, the REP13E12 family, is described that is present in seven copies on the M. tuberculosis H37Rv chromosome and which contains a probable phage attachment site. This study therefore offers an insight into the possible role of ISs and repetitive elements in the evolution of the M. tuberculosis genome, as well as identifying genetic markers that may be useful for phylogenetic and epidemiological analysis of the tubercle complex.