Journal of Molecular Evolution

Different Evolutionary Strategies for the Origin of Caspase-1 Inhibitors.

Publication Date: 2008 May 14 PMID: 18473111
Authors: da Cunha, J. P. - Galante, P. A. - de Souza, S. J.
Journal: J Mol Evol

Caspase 1 (CASP-1) inhibitors share sequence similarity to CASP-1 itself and are all mapped to chr11q22.3. Here we show that these inhibitors are all products of a series of gene duplications that occurred at this locus after the divergence between human and mouse. Surprisingly, stop codons originated independently in all duplicated copies to generate CARD-only proteins with inhibitory activity. We discuss this evolutionary model in the context of both neo- and subfunctionalization.

post to: CiteULike

The Evolution of Alternative Splicing in the Pax Family: The View from the Basal Chordate Amphioxus.

Publication Date: 2008 May 14 PMID: 18473110
Authors: Short, S. - Holland, L. Z.
Journal: J Mol Evol

Pax genes encode transcription factors critical for metazoan development. Large-scale gene duplication with subsequent gene losses during vertebrate evolution has resulted in two human genes for each of the Pax1/9, Pax3/7, and Pax4/6 subfamilies and three for the Pax2/5/8 subfamily, compared to one each in the cephalochordate amphioxus. In addition, alternative splicing occurs in vertebrate Pax transcripts from all four subfamilies, and many splice forms are known to have functional importance. To better understand the evolution of alternative splicing within the Pax family, we systematically surveyed transcripts of the four amphioxus Pax genes. We have found alternative splicing in every gene. Comparisons with vertebrates suggest that the number of alternative splicing events per gene has not decreased following duplication; there are comparable levels in the four amphioxus Pax genes as in each gene of the equivalent vertebrate families. Thus, the total number of isoforms for the nine vertebrate genes is considerably higher than for the four amphioxus genes. Most alternative splicing events appear to have arisen since the divergence of amphioxus and vertebrate lineages, suggesting that differences in alternative splicing could account for divergent functions of the highly conserved Pax genes in both lineages. However, several events predicted to dramatically alter known functional domains are conserved between amphioxus and vertebrates, suggestive of a common chordate function. Our results, together with previous studies of vertebrate Pax genes, support the theory that alternative splicing impacts functional motifs more than gene duplication followed by divergence.

post to: CiteULike

Polymorphism and Divergence at Three Duplicate Genes in Brassica nigra.

Publication Date: 2008 May 10 PMID: 18470551
Authors: Sjodin, P. - Hedman, H. - Kruskopf Osterberg, M. - Gustafsson, S. - Lagercrantz, U. - Lascoux, M.
Journal: J Mol Evol

The CONSTANS-like gene family has been shown to evolve exceptionally fast in Brassicaceae. In the present study we analyzed sequence polymorphism and divergence of three genes from this family: COL1 (CONSTANS-LIKE 1) and two copies of CO (CONSTANS), COa and COb, in B. nigra. There was a significant fourfold difference in overall nucleotide diversity among the three genes, with BniCOb having twice as much variation as BniCOL1, which in turn was twice as variable as BniCOa. The ratio of nonsynonymous-to-synonymous substitutions (dN/dS) was high for all three genes, confirming previous studies. While we did not detect evidence of selection at BniCOa and BniCOb, there was a significant excess of polymorphic synonymous mutations in a McDonald-Kreitman test comparing COL1 in B. nigra and A. thaliana. This is apparently the result of an increase in selective constraint on COL1 in B. nigra combined with a decrease in A. thaliana. In conclusion, a complex scenario involving both demography and selection seems to have shaped the pattern of polymorphism at the three genes.

post to: CiteULike

Positive Selection on HIV Accessory Proteins and the Analysis of Molecular Adaptation After Interspecies Transmission.

Publication Date: 2008 May 9 PMID: 18465165
Authors: Soares, A. E. - Soares, M. A. - Schrago, C. G.
Journal: J Mol Evol

Studies examining positive selection on accessory proteins of HIV are rare, although these proteins play an important role in pathogenesis in vivo. Moreover, despite the biological relevance of analyses of molecular adaptation after viral transmission between species, the issue is still poorly studied. Here we present evidence that accessory proteins are subjected to positive selective forces exclusively in HIV. This scenario suggests that accessory protein genes are under adaptive evolution in HIV clades, while in SIVcpz such a phenomenon could not be detected. As a result, we show that comparative studies are critical to carry out functional investigation of positively selected protein sites, as they might help to achieve a better comprehension of the biology of HIV pathogenesis.

post to: CiteULike

Complete Sequence of the Duckweed (Lemna minor) Chloroplast Genome: Structural Organization and Phylogenetic Relationships to Other Angiosperms.

Publication Date: 2008 May 8 PMID: 18463914
Authors: Mardanov, A. V. - Ravin, N. V. - Kuznetsov, B. B. - Samigullin, T. H. - Antonov, A. S. - Kolganova, T. V. - Skyabin, K. G.
Journal: J Mol Evol

The complete nucleotide sequence of the duckweed (Lemna minor) chloroplast genome (cpDNA) was determined. The cpDNA is a circular molecule of 165,955 bp containing a pair of 31,223-bp inverted repeat regions (IRs), which are separated by small and large single-copy regions of 89,906 and 13,603 bp, respectively. The entire gene pool and relative positions of 112 genes (78 protein-encoding genes, 30 tRNA genes, and 4 rRNA genes) are almost identical to those of Amborella trichopoda cpDNA; the minor difference is the absence of infA and ycf15 genes in the duckweed cpDNA. The inverted repeat is expanded to include ycf1 and rps15 genes; this pattern is unique and does not occur in any other sequenced cpDNA of land plants. As in basal angiosperms and eudicots, but not in other monocots, the borders between IRs and a large single-copy region are located upstream of rps19 and downstream of trnH, so that trnH is not included in IRs. The model of rearrangements of the chloroplast genome during the evolution of monocots is proposed as the result of the comparison of cpDNA structures in duckweed and other monocots. The phylogenetic analyses of 61 protein-coding genes from 38 plastid genome sequences provided strong support for the monophyly of monocots and position of Lemna as the next diverging lineage of monocots after Acorales. Our analyses also provided support for Amborella as a sister to all other angiosperms, but in the bayesian phylogeny inference based on the first two codon positions Amborella united with Nymphaeales.

post to: CiteULike

Mathematical Modelling of Mycobacterium tuberculosis VNTR Loci Estimates a Very Slow Mutation Rate for the Repeats.

Publication Date: 2008 May 6 PMID: 18458805
Authors: Grant, A. - Arnold, C. - Thorne, N. - Gharbia, S. - Underwood, A.
Journal: J Mol Evol

Minisatellites are highly variable tandem repeats used for over 20 years in humans for DNA fingerprinting. In prokaryotes fingerprinting techniques exploiting VNTR (variable number of tandem repeats) polymorphisms have become widely used recently in bacterial typing. However although many investigations into the mechanisms underlying minisatellite variation in humans have been performed, relatively little is known about the processes that mediate bacterial minisatellite polymorphism. An understanding of this is important since it will influence how the results from VNTR experiments are interpreted. The minisatellites of Mycobacterium tuberculosis are well characterized since they are some of the few polymorphic loci in what is otherwise a very homogeneous organism. Using VNTR results from a well-defined and characterized set of M. tuberculosis strains we show that the repeats at a locus are likely to evolve by stepwise contraction or expansion in the number of repeats. A stochastic continuous-time population mathematical model was developed to simulate the evolution of the repeats. This allowed estimation of the tendency of the repeats to increase or decrease and the rate at which they change. The majority of loci tend to lose rather than gain repeats. All of the loci mutate extremely slowly, with an average rate of 2.3 x 10(-8), which is 350 times slower than that of a set of VNTR repeats with similar diversity observed experimentally in Escherichia coli. This suggests that the VNTR profile of a strain of M. tuberculosis will be indicative of its clonal lineage and will be unlikely to vary in epidemiologically-related strains.

post to: CiteULike

On the Physical Basis of the Amino Acid Polar Requirement.

Publication Date: 2008 Apr 29 PMID: 18443736
Authors: Mathew, D. C. - Luthey-Schulten, Z.
Journal: J Mol Evol

Understanding how codons became associated with their specific amino acids is fundamental to deriving a theory for the origin of the genetic code. Carl Woese and coworkers designed a series of experiments to test associations between amino acids and nucleobases that may have played a role in establishing the genetic code. Through these experiments it was found that a property of amino acids called the polar requirement (PR) is correlated with the organization of the codon table. No other property of amino acids has been found that correlates with the codon table as well as PR, indicating that PR is uniquely related to the modern genetic code. Using molecular dynamics simulations of amino acids in solutions of water and dimethylpyridine used to experimentally measure PR, we show that variations in the partitioning between the two phases as described by radial distribution functions correlate well with the measured PRs. Partition coefficients based on probability densities of the amino acids in each phase have the linear behavior with base concentration as suggested by PR experiments.

post to: CiteULike

Early Evolution of Histone Genes: Prevalence of an 'Orphon' H1 Lineage in Protostomes and Birth-and-Death Process in the H2A Family.

Publication Date: 2008 Apr 29 PMID: 18443735
Authors: Gonzalez-Romero, R. - Ausio, J. - Mendez, J. - Eirin-Lopez, J. M.
Journal: J Mol Evol

The study of histone evolution has experienced a rebirth, for two main reasons: the identification of new essential histone variants responsible for regulating chromatin dynamics and the subsequent contradictions posed by this variability as it pertains to their long-term evolution process. Although different evolutionary models (e.g., birth-and-death evolution, concerted evolution) may account for the observed divergence of histone genes, conclusive evidence is lacking (e.g., histone H1) or totally nonexistent (e.g., histone H2A). While most of the published work has focused on deuterostomes, very little is known about the diversification and functional differentiation mechanisms followed by histone protein subtypes in protostomes, for which histone variants have only been recently described. In this study, we identify linker and core histone genes in three clam species. Our results demonstrate the prevalence of an 'orphon' H1 lineage in molluscs, a group in which the protostome H1 and sperm nuclear basic proteins are on the verge of diversification. They share an early monophyletic origin with vertebrate-specific variants prior to the differentiation between protostomes and deuterostomes. Given the intringuing evolutionary features of the histone H1 family, we have evaluated the relative importance of gene conversion, point mutation, and selection in maintaining the diversity found among H2A subtypes in eukaryotes. We show evidence for the first time that the long-term evolution of this family is not subject to concerted evolution but, rather, to a gradual evolution following a birth-and-death model under a strong purifying selection at the protein level.

post to: CiteULike