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• The Bacillaceae-1 RNA motif consists of two distinct classes. • Reverse complementary B-1 structure upstream of 16S rRNA has one stable motif. • Intergenic B-1 motifs have high structure diversity and may act as structural switch. Non-coding RNAs are key regulatory players in bacteria. Many computationally predicted non-coding RNAs, however, lack functional associations. An example is the Bacillaceae-1 RNA motif, whose Rfam model consists of two hairpin loops. We find the motif conserved in nine of 13 non-pathogenic strains of the genus Bacillus but only in one pathogenic strain. To elucidate functional characteristics, we studied 118 hits of the Rfam model in 11 Bacillus spp. and found two distinct classes based on the ensemble diversity of their RNA secondary structure and the genomic context concerning the ribosomal RNA (rRNA) cluster. Forty hits are associated with the rRNA cluster, of which all 19 hits upstream flanking of 16S rRNA have a reverse complementary structure of low structural diversity. Fifty-two hits have large ensemble diversity, of which 38 are located between two coding genes. For eight hits in Bacillus subtilis , we investigated public expression data under various conditions and observed either the forward or the reverse complementary motif expressed. Five hits are associated with the rRNA cluster. Four of them are located upstream of the 16S rRNA and are not transcriptionally active, but instead, their reverse complements with low structural diversity are expressed together with the rRNA cluster. The three other hits are located between two coding genes in non-conserved genomic loci. Two of them are independently expressed from their surrounding genes and are structurally diverse. In summary, we found that Bacillaceae-1 RNA motifs upstream flanking of ribosomal RNA clusters tend to have one stable structure with the reverse complementary motif expressed in B. subtilis. In contrast, a subgroup of intergenic motifs has the thermodynamic potential for structural switches. [ABSTRACT FROM AUTHOR]

The nephelauxetic phenomenon is reviewed. So is the newest formulation of the Slater–Condon–Shortley model (SCS) for the multiplet term energies of atomic dq ions. This model is expressed as a sum of products of empirical parameters and their associated coefficient operators. The orthogonal-operators formalism is used by choosing Jørgensen''s spin-pairing energy parameter D as one of the repulsion parameters when the other parameter required by the SCS model is the Racah parameter B. By restricting the coefficient operators further so as to make them orthonormal, B changes into the new parameter E=(21/4)B. D accounts for the energy separation of eigenstates with different spin and/or seniority, E for the final separation into the spatially different eigenstates. The numerical values of D and E exhibit directly the relative contributions of D and E to the average configurational splitting. The parameter set {D, E} is equivalent to the SCS set {F2, F4} as well as to the Racah set {C, B} even though these sets are not associated with orthogonal operators so that cross products, as for instance CB, enter the expressions for the average configurational splitting. Moreover, neither conventional parameter set provides a visualizable interpretation of the energetic functioning of its parameters upon the eigenstate energy separations. The symmetry problem of the two-electron part of Kohn–Sham DFT is discussed in the framework of the SCS model. With the future perspective of mimicking ligand-field theory and, in particular, of dealing with the full nephelauxetic phenomenon non-empirically, the atomic part of the phenomenon is handled by calculation of the parameters D and E successfully for numerous gaseous ions with 3dq configurations. The Amsterdam Density Functional package (ADF) has been used in a two-step procedure. First, all the Kohn–Sham self-consistent field d-orbitals of the 3dq configurations as well as all the inner core orbitals were determined using population numbers of q/10 for all the 3d-spin–orbitals, that is, by doing the average-of-configuration calculation. Secondly, all these orbitals were frozen in all the subsequent calculations on the same system. Here density distributions of α and β electrons were defined by integer occupation numbers of d-spin–orbitals corresponding to single Slater determinants. On grounds of principle, complex orbitals were found not to be usable. The ADF energy associated with a real determinant was—apart from an additive constant—taken to correspond to the expectation value of the interelectronic repulsion operator acting on the dq part of this determinant. A characteristic property of the method is that the energy is expressed by a sum over contributions from the Coulomb and the exchange-correlation functional. It has turned out that for real d-orbitals both of these terms independently obey the symmetry restrictions as well as the special SCS restrictions of the dq assumption. However, the two functionals are not commensurable. They give different parametric results. Nevertheless, by averaging the total energy results from using a gradient-corrected (GC) set of functionals over the configuration dq, values for the SCS parameters that are better than those of Hartree–Fock calculations are obtained. In the local density approximation (LDA) the exchange-correlation functionals were found to provide the same energy for all real Slater determinants with the same value for MS, which means that the exchange-correlation part of the energy corresponds to B=E=0. However, the Coulomb functional invariably exaggerates the values of the E parameter so that LDA functionals end up giving fairly reasonable values of E, as well as D. We have obtained a complete bridge between KS-DFT in the form of ADF and the atomic part of ligand-field theory. [Copyright &y& Elsevier]