The l box is a conserved regulatory motif which is found upstream of plant genes (rbcS, cab and nia) whose transcription is regulated by light and the circadian clock. Gel retardation and UV cross-linking assays were used to resolve two different groups of I box binding factors (IBFs) in tomato nuclear extracts. Active components of the first group (IBF-1) recognize the l box of the light-responsive rbcS promoter; one factor within this group, IBF-1a, also recognizes the adjacent G box, which has been shown previously to bind a different class of plant transcription factors, the G box binding factors (GBFs). To the limit of experimental resolution, IBF-1a and GBF compete for the same nucleotides on the G box. Nevertheless, these two activities are biochemically and immunologically distinct. The relative abundance of IBF-1a shows a vast decrease in dark-adapted plants. Factors in the second group (IBF-2), recognize the l box of the nia promoter, which is regulated both by light and the circadian clock; one factor within this group, IBF-2a, also binds the l box of a second promoter showing similar regulation, the cab promoter. The IBF-2a binding sites on the cab and nia promoters show extensive homology to a circadian clock-responsive promoter element from wheat. The abundance of IBF-2a is diurnally regulated and shows a dramatic induction around the onset of the light period. Transfer of the plants in continuous darkness demonstrates that this induction is under the control of a circadian clock.(ABSTRACT TRUNCATED AT 250 WORDS)

The SWI2/SNF2 gene family has been implicated in a wide variety of processes, involving regulation of DNA structure and chromatin configuration, mitotic chromosome segregation, and DNA repair. Here we report the characterization of the Zbu1 gene, also known as HIP116, located on human chromosome band 3q25, which encodes a DNA-binding member of this superfamily. Zbu1 was isolated in this study by its affinity for a site in the myosin light chain 1/3 enhancer. The protein has single-stranded DNA-dependent ATPase activity, includes seven helicase motifs, and a RING finger motif that is shared exclusively by the RAD5, spRAD8, and RAD16 family members. During mouse embryogenesis, Zbu1 transcripts are detected relatively late in fetal development and increase in neonatal stages, whereas the protein accumulates asynchronously in heart, skeletal muscle, and brain. In adult human tissues, alternatively spliced Zbu1 transcripts are ubiquitous with highest expression in these tissues. Gene expression is also dramatically induced in human tumor lines and in Li-Fraumeni fibroblast cultures, suggesting that it is aberrantly regulated in malignant cells. The developmental profile of Zbu1 gene expression and the association of the protein with a tissue-specific transcriptional regulatory element distinguish it from other members of the SWI2/SNF2 family and suggest novel roles for the Zbu1 gene product.

The EF-2 coding genes of the Archaea Pyrococcus woesei and Desulfuoccus mobilis were cloned and sequenced. Global phylogenies were inferred by alternative tree-makig methods from available EF-2(G) sequence data and contrasted with phylogenies constructed from the more conserved but shorter EF-la(Tu) sequences. Both the monophyly (sensu Henig) of Archaea and their subdivision into the kingdoms Crenarchaeota and Euryarchaeota are cnsendy inferred by analysis of EF-2(G) sequences, usually at a high bootstrap confidence level. In contras, EF-la(Tu) phylogenies tend to be inconsistent with one another and show low bootstrap confidence levels. While evolutionary distance and DNA maximum parsimony analyses of EF-la(Tu) sequences do show archaeal monophyly, protein p ony and DNA maximum-likelihood analyses of these data do not. In no case, however, do any of the tree topologies inferred from EFla(Tu) sequence analyses receive si nt bootstrap support.Phylogenies spanning extant life-forms have been reconstructed from molecular sequence data by using small-and large-subunit rRNAs (1, 2), RNA polymerase core subunits (3), H+-ATPase a and (3 subunits (4, 5), and the two elongation factors EF-la (and its eubacterial homolog EF-Tu), which is involved in aminoacyl-tRNA binding (6, 7), and EF-2 (and its eubacterial homolog EF-G), which is involved in peptidyl-tRNA translocation (8).In that the stem leading to the archaeal branch in a global tree is always significantly shorter than those that lead to the Bacteria or the Eucarya, it is not surprising that the various tree-making methods applied to various molecular types do not always yield a (statistically significant) monophyletic grouping for the Archaea. This has led rightly or wrongly to the conclusion by some that the Archaea are not a monophyletic grouping (sensu Hennig) (9,10). Phylogenies based upon EF-la(Tu) are a good case in this point: Although most analyses (6, 7) yield a monophyletic archaeal grouping, the archaeal stem (joining the Archaea to the other lineages) is more than an order of magnitude shorter than its bacterial or eucaryal counterparts (6, 7). And some EF-la(Tu) analyses indeed have given paraphyletic archaeal groupings (11). Given the far-reaching implications of the topology of the global phylogenetic tree, it is important to understand and resolve these differences.Here we compare phylogenies inferred by various methods from the relatively short and conserved sequences of the EF-la(Tu) type (about 400 aa) to those inferred from its longer, less conserved counterpart, of the EF-2(G) type (about 700 aa). To increase the rather meager collection of archaeal EF-2 sequences we have cloned and sequenced the EF-2 coding genes from the sulfur-dependent Archaea Pyrococcus woesei and Desulfurococcus mobilis. § Phylogenetic trees have been inferred by using evolutionary (sequence) distance, parsimony, and maximum-likelihood methods, based either upon the first and second codon positions in the alignments or upon the second positions only. It is clear ...

Phylogenies were inferred from both the gene and the protein sequences of the translational elongation factor termed EF-2 (for Archaea and Eukarya) and EF-G (for Bacteria). All treeing methods used (distance-matrix, maximum likelihood, and parsimony), including evolutionary parsimony, support the archaeal tree and disprove the "eocyte tree" (i.e., the polyphyly and paraphyly of the Archaea). Distance-matrix trees derived from both the amino acid and the DNA sequence alignments (first and second codon positions) showed the Archaea to be a monophyletic-holophyletic grouping whose deepest bifurcation divides a Sulfolobus branch from a branch comprising Methanococcus, Halobacterium, and Thermoplasma. Bootstrapped distance-matrix treeing confirmed the monophyly-holophyly of Archaea in 100% of the samples and supported the bifurcation of Archaea into a Sulfolobus branch and a methanogen-halophile branch in 97% of the samples. Similar phylogenies were inferred by maximum likelihood and by maximum (protein and DNA) parsimony. DNA parsimony trees essentially identical to those inferred from first and second codon positions were derived from alternative DNA data sets comprising either the first or the second position of each codon. Bootstrapped DNA parsimony supported the monophyly-holophyly of Archaea in 100% of the bootstrap samples and confirmed the division of Archaea into a Sulfolobus branch and a methanogen-halophile branch in 93% of the bootstrap samples. Distance-matrix and maximum likelihood treeing under the constraint that branch lengths must be consistent with a molecular clock placed the root of the universal tree between the Bacteria and the bifurcation of Archaea and Eukarya. The results support the division of Archaea into the kingdoms Crenarchaeota (corresponding to the Sulfolobus branch and Euryarchaeota). This division was not confirmed by evolutionary parsimony, which identified Halobacterium rather than Sulfolobus as the deepest offspring within the Archaea.

To dissect the molecular mechanisms conferring positional information in skeletal muscles, we characterized the control elements responsible for the positionally restricted expression patterns of a muscle-specific transgene reporter, driven by regulatory sequences from the MLC1/3 locus. These sequences have previously been shown to generate graded transgene expression in the segmented axial muscles and their myotomal precursors, fortuitously marking their positional address. An evolutionarily conserved E box in the MLC enhancer core, not recognized by MyoD, is a target for a nuclear protein complex, present in a variety of tissues, which includes Hox proteins and Zbu1, a DNA-binding member of the SW12/SNF2 gene family. Mutation of this E box in the MLC enhancer has only a modest positive effect on linked CAT gene expression in transfected muscle cells, but when introduced into transgenic mice the same mutation elevates CAT transgene expression in skeletal muscles, specifically releasing the rostral restriction on MLC-CAT transgene expression in the segmented axial musculature. Increased transgene activity resulting from the E box mutation in the MLC enhancer correlates with reduced DNA methylation of the distal transgenic MLC1 promoter as well as in the enhancer itself. These results identify an E box and the proteins that bind to it as a positional sensor responsible for regional differences in axial skeletal muscle gene expression and accessibility.