Positional Homology in Bacterial Genomes

In comparative genomic studies, syntenic groups of homologous sequence in the same order have been used as supplementary information that can be used in helping to determine the orthology of the compared sequences. The assumption is that ortholo-gous gene copies are more likely to share the same genome positions and share the same gene neighbors. In this study we have defined positional homologs as those that also have homologous neighboring genes and we investigated the usefulness of this distinction for bacterial comparative genomics. We considered the identification of positionaly homologous gene pairs in bacterial genomes using protein and DNA sequence level alignments and found that the positional homologs had on average relatively lower rates of substitution at the DNA level (synonymous substitutions) than duplicate homologs in different genomic locations, regardless of the level of protein sequence divergence (measured with non-synonymous substitution rate). Since gene order conservation can indicate accuracy of orthology assignments, we also considered the effect of imposing certain alignment quality requirements on the sensitivity and specificity of identification of protein pairs by BLAST and FASTA when neighboring information is not available and in comparisons where gene order is not conserved. We found that the addition of a stringency filter based on the second best hits was an efficient way to remove dubious ortholog identifications in BLAST and FASTA analyses. Gene order conservation and DNA sequence homology are useful to consider in comparative genomic studies as they may indicate different orthology assignments than protein sequence homology alone

MSH3 polymorphisms and protein levels affect CAG repeat instability in huntington's disease mice

Expansions of trinucleotide CAG/CTG repeats in somatic tissues are thought to contribute to ongoing disease progression through an affected individual's life with Huntington's disease or myotonic dystrophy. Broad ranges of repeat instability arise between individuals with expanded repeats, suggesting the existence of modifiers of repeat instability. Mice with expanded CAG/CTG repeats show variable levels of instability depending upon mouse strain. However, to date the genetic modifiers underlying these differences have not been identified. We show that in liver and striatum the R6/1 Huntington's disease (HD) (CAG)~100 transgene, when present in a congenic C57BL/6J (B6) background, incurred expansion-biased repeat mutations, whereas the repeat was stable in a congenic BALB/cByJ (CBy) background. Reciprocal congenic mice revealed the Msh3 gene as the determinant for the differences in repeat instability. Expansion bias was observed in congenic mice homozygous for the B6 Msh3 gene on a CBy background, while the CAG tract was stabilized in congenics homozygous for the CBy Msh3 gene on a B6 background. The CAG stabilization was as dramatic as genetic deficiency of Msh2. The B6 and CBy Msh3 genes had identical promoters but differed in coding regions and showed strikingly different protein levels. B6 MSH3 variant protein is highly expressed and associated with CAG expansions, while the CBy MSH3 variant protein is expressed at barely detectable levels, associating with CAG stability. The DHFR protein, which is divergently transcribed from a promoter shared by the Msh3 gene, did not show varied levels between mouse strains. Thus, naturally occurring MSH3 protein polymorphisms are modifiers of CAG repeat instability, likely through variable MSH3 protein stability. Since evidence supports that somatic CAG instability is a modifier and predictor of disease, our data are consistent with the hypothesis that variable levels of CAG instability associated with polymorphisms of DNA repair genes may have prognostic implications for various repeat-associated diseases

Corresponding author:

(PMB), ribosomal RNA (rRNA), transfer RNA (tRNA), Hidden Markov Model (HMM) 1 Copyright (c) 2003 Society for Molecular Biology and Evolution Empirical models of substitution are often used in protein sequence analysis because the large alphabet of amino acids requires that many parameters be estimated in all but the simplest parametric models. When information about structure is used in the analysis of substitutions in structured RNA, a similar situation occurs. The number of parameters necessary to adequately describe the substitution process increases in order to model the substitution of paired bases. We have developed a method to obtain substitution rate matrices empirically from RNA alignments that include structural information in the form of base pairs. Our data consisted of alignments from the European ribosomal RNA database of Bacterial and Eukaryotic Small Subunit and Large Subunit ribosomal RNA (Wuyts et al., 2001a; Wuyts et al., 2002). Using secondary structural information, we converted each sequence in the alignments into

BIOINFORMATICS ORIGINAL PAPER doi:10.1093/bioinformatics/btm114 Sequence analysis

A fast and flexible approach to oligonucleotide probe design for genomes and gene familie

Structural and sequence analysis of MSH3.

<p>A: Multiple sequence alignment of MSH3. Jalview created visualization <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003280#pgen.1003280-Clamp1" target="_blank">[120]</a> using the first 500 amino acids of the mouse B6 MSH3 (NP_034959.2). Conservation values and consensus sequence are based on alignment of <i>S. cerevisiae</i> Msh3p, <i>E. coli</i> MutS and 17 mammalian MSH3 homologs; values range from 0–9, where 0 is lowest and 9 is the highest. Protein interacting domains indicated pertain to those regions of the human MSH3 protein. This panel only shows an abbreviated set of the species of MSH3 sequence, the full set analysed is shown in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003280#pgen.1003280.s005" target="_blank">Figure S5</a>. B: MSH3 variant within β-turn. The T321I variant occurs within a Type I β-turn, as determined by specific backbone turn angles <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003280#pgen.1003280-Kabsch1" target="_blank">[117]</a>, <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003280#pgen.1003280-Venkatachalam1" target="_blank">[118]</a> from the human MSH3 structure (3THW_B). Top left: hMSH3 tube diagram of Cα atoms of β-turn (blue), <i>i</i>+2 (T) residue (red) and additional three residues on N- and C-terminal ends (green). Bottom left table shows the β-turn propensity is relatively strong throughout MutS/MSH3 homologs, while the CBy variant (Isoleucine at <i>i+2</i> position) is extremely disfavored (table bottom left) <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003280#pgen.1003280-Hutchinson1" target="_blank">[69]</a>. Right: Ball and stick diagram of contact sites of Asp (D) and Thr (T) residues in β-turn with residues 194 and 214 respectively. Line diagram of Thr (T) hydroxyl group contact with neighbouring Threonine residue at position 365. The absence of the Threonine hydroxyl group may be important to stabilizing the β-turn itself, and/or may change the conformation of the turn, potentially disrupting distant contacts important for proper protein folding. MSH3 visualizations created using PyMol (PyMOL Molecular Graphics System, Version 1.2r3pre, Schrödinger, LLC).</p

Representative CAG repeat distributions from reciprocal <i>Msh3</i> congenic lines of mice.

<p>Typical GeneScan traces for sizing of the CAG repeat as outlined in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003280#pgen-1003280-g001" target="_blank">Figure 1B</a>. Liver (A) and Striatum (B) from 16–20 week old R6/1 transgenic mice showing the effect of homozygosity at the <i>Msh3</i> locus on the pattern of expansion in the reciprocal congenic mice. Regardless of genetic background, CBy homozygosity at the congenic locus results in loss of somatic expansion, while B6 homozygosity is permissive of somatic expansion.</p