Synonymous substitutions are clustered in enterobacterial genes

The spatial distribution of synonymous substitutions in enterobacterial genes is investigated. It is shown that synonymous substitutions are significantly clustered in such a way that a synonymous substitution in one codon elevates the rate of synonymous substitution in an adjacent codon by about 10%. The level of clustering does not appear to be related to the level of gene expression, and it is restricted to a range of two or three codons. There are at least three possible explanations: (1) sequence-directed mutagenesis, (2) recombination, and (3) selection.     

Two regions of M13 phage genome hybridizing with human DNA are similar to several keratin genes.

DNA from two regions of the phage M13 genome hybridizes with DNA restriction fragments from genomes of various species including man [15, 20]. As the pattern of hybridization is individual-specific, this phage M13 probe can be used for DNA fingerprinting. We demonstrate here that the regions of many keratin genes coding for glycine-rich parts of C and N end domains are very similar to the phage M13 probe, and this similarity may be responsible for hybridization.     

Histone acetylation and chromatin remodeling are required for UV-B-dependent transcriptional activation of regulated genes in maize

The nuclear proteomes of maize (Zea mays) lines that differ in UV-B tolerance were compared by two-dimensional gel electrophoresis after UV light treatment. Differential accumulation of chromatin proteins, particularly histones, constituted the largest class identified by mass spectrometry. UV-B-tolerant landraces and the B73 inbred line show twice as many protein changes as the UV-B-sensitive b, pl W23 inbred line and transgenic maize expressing RNA interference constructs directed against chromatin factors. Mass spectrometic analysis of posttranslational modifications on histone proteins demonstrates that UV-B-tolerant lines exhibit greater acetylation on N-terminal tails of histones H3 and H4 after irradiation. These acetylated histones are enriched in the promoter and transcribed regions of the two UV-B-upregulated genes examined; radiation-sensitive lines lack this enrichment. DNase I and micrococcal nuclease hypersensitivity assays indicate that chromatin adopts looser structures around the selected genes in the UV-B-tolerant samples. Chromatin immunoprecipitation experiments identified additional chromatin factor changes associated with the nfc102 test gene after UV-B treatment in radiation-tolerant lines. Chromatin remodeling is thus shown to be a key process in acclimation to UV-B, and lines deficient in this process are more sensitive to UV-B.     

Nuclear genes that encode mitochondrial proteins for DNA and RNA metabolism are clustered in the Arabidopsis genome

The plant mitochondrial genome is complex in structure, owing to a high degree of recombination activity that subdivides the genome and increases genetic variation. The replication activity of various portions of the mitochondrial genome appears to be nonuniform, providing the plant with an ability to modulate its mitochondrial genotype during development. These and other interesting features of the plant mitochondrial genome suggest that adaptive changes have occurred in DNA maintenance and transmission that will provide insight into unique aspects of plant mitochondrial biology and mitochondrial-chloroplast coevolution. A search in the Arabidopsis genome for genes involved in the regulation of mitochondrial DNA metabolism revealed a region of chromosome III that is unusually rich in genes for mitochondrial DNA and RNA maintenance. An apparently similar genetic linkage was observed in the rice genome. Several of the genes identified within the chromosome III interval appear to target the plastid or to be targeted dually to the mitochondria and the plastid, suggesting that the process of endosymbiosis likely is accompanied by an intimate coevolution of these two organelles for their genome maintenance functions.     

Trinucleotide repeats are clustered in regulatory genes in Saccharomyces cerevisiae

The genome of Saccharomyces cerevisiae contains numerous unstable microsatellite sequences. Mononucleotide and dinucleotide repeats are rarely found in ORFs, and when present in an ORF are frequently located in an intron or at the C terminus of the protein, suggesting that their instability is deleterious to gene function. DNA trinucleotide repeats (TNRs) are found at a higher-than-expected frequency within ORFs, and the amino acids encoded by the TNRs represent a biased set. TNRs are rarely conserved between genes with related sequences, suggesting high instability or a recent origin. The genes in which TNRs are most frequently found are related to cellular regulation. The protein structural database is notably lacking in proteins containing amino acid tracts, suggesting that they are not located in structured regions of a protein but are rather located between domains. This conclusion is consistent with the location of amino acid tracts in two protein families. The preferred location of TNRs within the ORFs of genes related to cellular regulation together with their instability suggest that TNRs could have an important role in speciation. Specifically, TNRs could serve as hot spots for recombination leading to domain swapping, or mutation of TNRs could allow rapid evolution of new domains of protein structure.     

Arabidopsis rbcS genes are differentially regulated by light.

Individual members of the Arabidopsis thaliana ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit (rbcS) gene family are differentially regulated by light of different qualities. In 10-d-old etiolated seedlings, the expression of only three of the four genes is under inductive phytochrome control. rbcS mRNA levels reach a maximum (3- to 5-fold higher than the dark level) about 6 h after a red light pulse, but the rate of decay differs among the genes. Moreover, rbcS 2B requires a higher fluence for induction. At early stages of development, rbcS 1A, 2B, and 3B are highly expressed in the dark and cannot be further induced by red light, indicating a developmental component in the overall regulatory mechanism. Continuous light experiments indicate that high-irradiance responses may play a role in the induction of at least three of the four rbcS genes. Under conditions of phytochrome saturation, rbcS 1A is insensitive to blue light pulses, whereas among the three B locus genes, at least rbcS 3B appears to respond to a blue-light photoreceptor. These results add to the data suggesting that individual members of rbcS gene families in higher plants may be subject to a variety of differing regulatory mechanisms.     

Three sweet receptor genes are clustered in human Chromosome 1

A search of the human genome database led us to identify three human candidate taste receptors, hT1R1, hT1R2, and hT1R3, which contain seven transmembrane domains. All three genes map to a small region of Chromosome (Chr) 1. This region is syntenous to the distal end of Chr 4 in mouse, which contains the Sac (saccharin preference) locus that is involved in detecting sweet tastants. A genetic marker, DVL1, which is linked to the Sac locus, is within 1700 bp of human T1R3. Recently, the murine T1Rs and its human ortholog have been independently identified in combination as sweet and umami receptors near the Sac locus. All three hT1Rs genes are expressed selectively in human taste receptor cells in the fungiform papillae, consistent with their role in taste perception.