Isolation and chromosomal distribution of natural Z-DNA-forming sequences in Halobacterium halobium

Transcriptional profiling of the model Archaeon Halobacterium sp. NRC-1: responses to changes in salinity and temperature

Background

The model halophile Halobacterium sp. NRC-1 was among the first Archaea to be completely sequenced and many post-genomic tools, including whole genome DNA microarrays are now being applied to its analysis. This extremophile displays tolerance to multiple stresses, including high salinity, extreme (non-mesophilic) temperatures, lack of oxygen, and ultraviolet and ionizing radiation.

Results

In order to study the response of Halobacterium sp. NRC-1 to two common stressors, salinity and temperature, we used whole genome DNA microarrays to assay for changes in gene expression under differential growth conditions. Cultures grown aerobically in rich medium at 42°C were compared to cultures grown at elevated or reduced temperature and high or low salinity. The results obtained were analyzed using a custom database and microarray analysis tools. Growth under salt stress conditions resulted in the modulation of genes coding for many ion transporters, including potassium, phosphate, and iron transporters, as well as some peptide transporters and stress proteins. Growth at cold temperature altered the expression of genes involved in lipid metabolism, buoyant gas vesicles, and cold shock proteins. Heat shock showed induction of several known chaperone genes. The results showed that Halobacterium sp. NRC-1 cells are highly responsive to environmental changes at the level of gene expression.

Conclusion

Transcriptional profiling showed that Halobacterium sp. NRC-1 is highly responsive to its environment and provided insights into some of the specific responses at the level of gene expression. Responses to changes in salt conditions appear to be designed to minimize the loss of essential ionic species and abate possible toxic effects of others, while exposure to temperature extremes elicit responses to promote protein folding and limit factors responsible for growth inhibition. This work lays the foundation for further bioinformatic and genetic studies which will lead to a more comprehensive understanding of the biology of a model halophilic Archaeon.

Periodicities of 10–11bp as Indicators of the Supercoiled State of Genomic DNA

DNA sequences contain information about the bendability and native conformation of DNA. For example, a repetition of certain dinucleotides at distances of 10-11bp supports wrapping around nucleosomes and supercoiled structures of bacterial DNA. We analyzed 86 eubacterial genomes, 16 archaea, and six genomes of higher eukaryotes. First, we discuss whether or not the observed periodicities represent indeed bendability signals. This claim is confirmed since: (1) dinucleotide signals are of comparable size to mononucleotide signals, (2) the signals are present in non-coding DNA as well, and (3) repeat masking has only a minor effect on 10-11bp periodicities. Moreover, the periodicities persist up to 150bp, comparable to the nucleosome size. We show that doublet peaks in Caenorhabditis elegans and some prokaryotes can be traced back to long-ranging modulations. In mammalian genomes, we find consistently spectral peaks as observed earlier in human chromosomes 20, 21 and 22. It has been shown in previous studies that archaea have periods of 10bp, whereas eubacteria exhibit 11bp periodicities. These differences reflect different supercoiled states of microbial DNA. Is the period of 10bp an archaeal or a thermophilic feature? This question is addressed by relating periodicities to optimal growth temperatures. It turns out that the archaea Methanopyrus kandleri (t(opt)=80 degrees C) and a Halobacterium strain (t(opt)=42 degrees C) both have longer periods of about 11bp. Eubacterial genomes have consistently periods around 11bp indicative of negative supercoiling.

In vitro and in vivo ligation-mediated polymerase chain reaction analysis of a polypurine/polypyrimidine sequence upstream of the mouse metallothionein-I gene

The mouse metallothionein-I homopurine/homopyrimidine (MT-I R/Y) sequence is a 128-base pair element located approximately 1.2 kilobase pairs upstream of the MT-I gene. Previous in vitro studies of this sequence in purified plasmids indicated the formation of a non-B DNA structure stabilized by acidic pH and negative supercoiling. We now present a detailed in vitro and in vivo analysis of the MT-I R/Y sequence using chemical probes of DNA structure and ligation-mediated polymerase chain reaction. In vivo analysis suggests neither profound base unpairing nor protein binding within the MT-I R/Y sequence before or after metal induction of MT-I. We conclude for this element that the propensity to adopt an unusual DNA structure in vitro does not imply the occurrence of such a structure in vivo. We were able to show both in purified genomic DNA and in vivo that only isolated thymines and the 3' terminal thymine in strings of consecutive thymines are modified significantly by KMnO(4), indicating an altered thymine accessibility pattern within the R/Y sequence. This KMnO(4) reactivity pattern is more consistent and predictable within the R/Y sequence when compared with flanking sequences. We propose a simple steric interference model to explain the observed pattern of KMnO(4) modification of thymines.

Transcription initiation in Archaea: facts, factors and future aspects

The basal apparatus for transcription initiation in Archaea is more closely related to the eukaryal than to the bacterial counterpart. The understanding of archaeal transcription initiation has been deepened by recent advances, which include genome sequencing, biochemical approaches and the structure determination of a protein DNA complex. Archaeal promoter elements, transcription factors, RNA polymerase and their interactions are discussed and compared with the eukaryal situation. It is emerging that transcription initiation is not uniform in Archaea. A minimal set of promoter elements and transcription factors is conserved, but the relative importance for transcription initiation can vary. Furthermore, additional basal transcription factors and promoter elements seem to be crucial in subgroups of Archaea. Finally, some aspects of global as well as gene-specific transcriptional regulation are discussed.

Structural and functional analysis of the phosphoenolpyruvate carboxylase gene from the purple nonsulfur bacterium Rhodopseudomonas palustris No. 7

The ppc gene, encoding phosphoenolpyruvate carboxylase (PEPC), from Rhodopseudomonas palustris No. 7 was cloned and sequenced. Primer extension analysis identified a transcriptional start site 42 bp upstream of the ppc initiation codon. An R. palustris No. 7 PEPC-deficient strain showed a slower doubling time compared with the wild-type strain either anaerobically in the light or aerobically in the dark, when pyruvate was used as a carbon source.