Previous IMEG Seminars and Abstracts:
Speaker: Dr. Eddie
Holmes- Department of Biology
Evolutionary Genomics of Influenza Virus."
Abstract: The current
interest in H5N1 avian influenza virus, and its potential threat to human health,
has generated a renewed interest in studies of influenza virus
evolution. Here I will show how the study of large amounts of
complete genome sequence data has shed light on the key patterns and
processes of influenza virus evolution. In particular, I will show
that reassortment among human influenza viruses is a far more important
process than generally envisaged and may have been important for a number
of “antigenic cluster jumps” in H3N2 influenza virus. I will also reveal
the evolutionary processes response for the dramatic and global rise in
resistance to adamantane drugs that occurred in recent months.
Through the intensive study of influenza virus in a single population – New
York state from 1995 to 2005 – I will show that rather than being characterized
by a single dominant lineage, the viruses present during any season
represent a small sample of global genetic diversity, with little antigenic
drift occurring over a season. The evolution of influenza A vírus is
therefore an episodic process, characterized by occasional selective
Holmes EC, Ghedin E, Miller N, Taylor J, Bao Y, St. George K,
Grenfell BT, Salzberg SL, Fraser CM, Lipman DJ & Taubenberger JK.
(2005). Whole genome analysis of human influenza A virus reveals multiple
persistent lineages and reassortment among recent H3N2 viruses. PLoS.Biol. 3(9),
Nelson MI, Simonsen L, Viboud C, Miller MA, Taylor J, St. George K,
Griesemer SB, Ghedin E, Sengamalay NA, Spiro DJ, Volkov I, Grenfell BT,
Lipman DJ, Taubenberger JK & Holmes EC. (2006). Stochastic processes
are key determinants of the short-term evolution of influenza A virus. PLoS
Path. 2, e125.
Izabela Makalowska- Department of Life Sciences
And Death of Gene Overlaps in Vertebrates."
Abstract: Several mechanisms have been proposed to explain gene
overlap origination. For instance, Keese and Gibbs suggested that
overlapping genes arise as a result of overprinting - a process of
generating new genes from preexisting nucleotide sequences. This process
supposedly took place after divergence of mammals from birds and
overlapping genes represent young, phylogeneticaly restricted genes
encoding proteins with diverse functions, and are therefore specialized to
the present life-style of the organism in which they are found. Shintani et
al. suggested that the overlap between genes ACAT2 (acetyl-Coenzyme
A acetyltransferase 2) and TCP1 (t-complex 1) arose during the
transition from therapsid reptiles to mammals as a result of translocation
accompanied (or followed) by loss of part of 3' URT including
polyadenylation signal and adoption of signals from the neighboring gene
locus. The ACAT2-TCP1 overlap evolution was placed, similarly
as in Keese anf Gibbs hypothesis, after the divergence of mammals from
birds. Dahary et al. places the origin of most vertebrate overlaps
much earlier. He found that human antisense genes have largely conserved
linkage in Fugu which may imply that big fraction of human overlapping
genes represents vertebrates' ancestral overlaps. However, our
previous study of human and mouse overlapping genes showed that even
between much closer related species overlaps are not that well conserved.
Here we present results of the comparative analysis of seven vertebrate
genomes: human, chimpanzee, mouse, rat, chicken, fugu, and zebrafish.
This comparative studies shows that many of the vertebrate gene overlaps
are not conserved and are lineage specific. On the other hand, this work
reveals new, not published before, cases of genes overlap conservation in
vertebrates. We also show new mechanisms of overlapping genes evolution and
demonstrate, for the first time, that evolutionary events could not only
lead to the new gene overlaps origin but also to the loss of an ancient
overlap. Therefore luck of strong overlaps conservation between even
closely related species may result not only from the origin of new, lineage
specific overlap but also be resulting from the loss of many overlaps in
Examples from our studies show that one of the major forces leading to
overlaps origin is a development of new splice variant, which could either
replace the ancient one or be just an addition to already present
variants. In addition, our study emphasizes that in order to fully
understand the evolution of overlapping genes one has to work in details on
References:Keese PK, Gibbs A:
Origins of genes: "big bang" or continuous creation? Proc
Natl Acad Sci U S A 1992, 89(20):9489-9493.
Shintani S, O'HUigin C, Toyosawa S, Michalova V, Klein J: Origin of gene
overlap: the case of TCP1 and ACAT2. Genetics 1999, 152(2):743-754.
Dahary D, Elroy-Stein O, Sorek R: Naturally occurring antisense:
transcriptional leakage or real overlap? Genome Res 2005, 15(3):364-368.
Veeramachaneni V, Makalowski W, Galdzicki M, Sood R, Makalowska I: Mammalian
overlapping genes: the comparative perspective. Genome Res 2004,
Zhang Y, Liu XS, Liu QR, Wei L: Genome-wide in silico identification and
analysis of cis natural antisense transcripts (cis-NATs) in ten species.
Nucleic Acids Res 2006, 34(12):3465-3475.
Wen-Ya Ko- Department of Biology
Title: "Within- and
between-species sequence variation in the Drosophila yakuba species
complex: adaptive protein evolution on A/T to G/C mutations."
Abstract: Fine-scale investigation of nucleotide changes is
critical for studying molecular evolution when the underlying evolutionary
parameter(s) fluctuates frequently on a gene tree and/or when patterns and
rates of nucleotide changes differ between polymorphism and divergence at
terminal lineages. Here, we studied within- and between-species
nucleotide variation from 19 loci (4530 codons) in D. yakuba and D.
santomea and from 6 loci (1414 codons) in D. teissieri.
Analysis of average number of polymorphic mutations per allele showed that
each terminal lineage contains a large proportion of polymorphic mutations
(0.69, 0.72, and 0.56 for D. teissieri, D. yakuba, and D.
santomea, respectively). The results suggest that polymorphic
mutations can have pronounced effects on inferring patterns of nucleotide
changes in a single-allele analysis where an excess of G/C à A/T
polymorphic mutations is observed in each species. Differences in ratios
of polymorphism to divergence between protein and different fitness classes
of synonymous mutations reveal evidence of adaptive protein evolution for
mutations from A/T à G/C, but not for mutations in the reverse
direction. Adaptive protein evolution on A/T à G/C mutations possibly
relates to selection discriminating a subset of amino acids or codons
during the processes of protein synthesis.
H., 1999 Within- and between-species DNA sequence variation and the
'footprint' of natural selection. Gene 238: 39-51.
AKASHI, H., W. Y. KO, S. PIAO, A. JOHN, P. GOEL et al., 2006
Molecular evolution in the Drosophila melanogaster species subgroup:
frequent parameter fluctuations on the timescale of molecular divergence.
Genetics 172: 1711-1726.
FAY, J. C., G. J. WYCKOFF and C. I. WU, 2002 Testing the neutral theory of
molecular evolution with genomic data from Drosophila. Nature 415:
SMITH, N. G., and A. EYRE-WALKER, 2002 Adaptive protein evolution in
Drosophila. Nature 415: 1022-1024.
Nikolas Nikolaidis- Department of Biology
Title: "The Land of
DANGER: an Ancient Developmental Superfamily."
Abstract: Developmental proteins in general and molecules involved
in cell differentiation in particular, play a pivotal role in the origin of
animal complexity and diversity. Therefore identifying and characterizing
the evolutionary history of such molecules is fundamentally important
towards understanding the origin of animal complexity and diversity. We
have recently identified a highly divergent developmental protein
superfamily (DANGER), which originated before the emergence of animals
(~850 million years ago) and experienced major expansion-contraction events
during metazoan evolution. Sequence analysis suggests that DANGER proteins
diverged via multiple mechanisms, including amino acid substitution, intron
gain and/or loss, and recombination. Divergence for DANGER proteins is
substantially greater than for the prototypic member of the superfamily
(Mab-21 family) and other developmental protein families (e.g., WNT
proteins). DANGER proteins are widely expressed and display
species-dependent tissue expression patterns, with many members having
roles in development. A member of this superfamily, DANGER1A, promotes the
differentiation and outgrowth of neuronal processes. Regulation of
development may be a universal function of DANGER family members. This
family provides a model system to investigate how rapid protein divergence
contributes to morphological complexity.
Chow KL, Hall DH, Emmons SW (1995) The mab-21 gene of
Caenorhabditis elegans encodes a novel protein required for choice of
alternate cell fates. Development 121: 3615-3626.
Davidson EH, Erwin DH (2006) Gene regulatory networks
and the evolution of animal body plans. Science 311: 796-800.
Kusserow A, Pang K, Sturm C, Hrouda M, Lentfer J et
Unexpected complexity of the Wnt gene family in a sea anemone. Nature 433:
Nikolaidis N, D Chalkia, DN Watkins, RK Barrow, SH
Snyder, van Rossum DB, RL Patterson. Ancient origin of a new developmental
superfamily DANGER. Plos ONE in press.
Technau U, Rudd S, Maxwell P, Gordon PM, Saina M et
al. (2005) Maintenance of ancestral complexity and non-metazoan genes in
two basal cnidarians. Trends
Genet 21: 633-639.
Rossum DB, Patterson RL, Cheung KH, Barrow RK, Syrovatkina V et al. (2006)
DANGER, a novel regulatory protein of inositol 1,4,5-trisphosphate-receptor
activity. J Biol Chem 281: 37111-37116.
Battistuzzi- Department of Biology-CANCELLED
Title: "Expanding the phylogeny and
timing of prokaryotes."
Abstract: Genome sequences
of Eubacteria and Archaebacteria have proven informative for the higher-level
phylogeny and timing of these organisms that dominated the biology of the
early Earth. As this tree of prokaryotes continues to grow with additional
sequences, it is possible to better understand how life coevolved with the
planetary environment. However, the chronological patterns and metabolic
innovations of prokaryote evolution ultimately rely on the phylogeny of
these groups, phylogeny that has proved challenging to define. Results from
the comparison of multiple phylogenetic trees (ML and distance methods for
amino acids and nucleotides data sets) suggest the presence of super-class
prokaryote groups, sub-class clusters, and classes that show a problematic
phylogenetic placement, leading to a partially resolved consensus tree.
They also show a consistent pattern of short internal branches that might
have consequences not only for the branching order but also the time
estimation of the major classes.
References: Ciccarelli, F.D.
et al. Toward automatic reconstruction of a highly resolved tree of life. Science
311, 1283-1287 (2006).
Hong Ma- Department of Biology
Title: "Highly variable
patterns of gene duplications in eukaryotic gene family evolution: possible
mechanisms and functional implications."
Abstract: Gene duplication is an important means of gene family
evolution, particularly in the birth-and-death model of gene family
evolution. We have examined the evolution of multiple gene families in
eukaryotes and uncovered a wide range of patterns of gene duplications.
Some gene families have very stable gene numbers over most, if not
all, of the eukarytic history; many gene families have
experienced moderate gene duplication rates. In addition, some gene
families have had very high rates of gene births in land plants,
particularly flowering plants. It has been proposed that both animals and
plants, as well as some fungi, have had large-scale genome duplication(s)
during their evolutionary history. If we accept this theory, then the
families that maintain stable gene number must eliminate duplicates shortly
after their birth. Conversely, the births in some gene families can
be explained by large-scale genone duplications. The gene families
with very rapid birth rates can be explained by additional mechanisms such
as tanden duplications and retro-transpositions. It is possible
that the functions of different genes can affect the fate of
duplicated genes, and the differential survival of the duplicates in turn
facilitate the evolution of specific characteristics. The effects of
other factors on gene family evolution is also discussed.
K, Leebens-Mack J, Weimin N, dePamphilis C W and Ma H. (2004) Highly
Heterogeneous Rates of Evolution in the SKP1 Gene Family in Plants and Animals:
Functional and Evolutionary Implications. Mol Biol Evol
Zahn L M,
Leebens-Mack J, DePamphilis C W, Ma H, and Theissen G. (2005) To B or Not
to B a Flower: The Role of DEFICIENS and GLOBOSA Orthologs in the Evolution
of the Angiosperms. J Here 96(3):225–240. Lin Z, Kong H, Nei M, Ma
H. (2006). Origin and evolution of the recA/RAD51 gene family:
Evidence for ancient gene duplication and endosymbiotic gene transfer. Proc
Natl Acad Sci USA, 103:10328-10333.
Meisel- Department of Biology
Title: "On the
Origin and Evolution of Segmentally Duplicated Genes in the Drosophila
Abstract: Gene duplication has been recognized as an important
evolutionary force for over three decades. The 12 sequenced Drosophila
genomes offer an excellent opportunity to study genome evolution, including
gene duplication. We identified recently duplicated genes in the Drosophila
pseudoobscura genome that arose via segmental duplication after the
divergence of D. pseudoobscura and D. melanogaster. The
relative orientations of paralogs, lengths of duplicated regions, and
sequences flanking duplicated regions provide insights into the molecular
mechanisms underlying segmental duplication in Drosophila genomes.
To gain a better understanding of the early evolution of duplicated genes,
we analyzed nucleotide and protein coding sequence divergence between
paralogs. I will present the results of these analyses of recently
segmentally duplicated genes in the D. pseudoobscura genome.
References: Moore and Purugganan.
2003. The early stages of duplicate gene evolution. PNAS 100:15682-25687.Richards,
et al. 2005. Comparative genome sequencing of Drosophila
pseudoobscura: chromosomal, gene, and cis-element evolution. Genome
Kvikstad -Department of Biology
macaque’s-eye view of human insertions and deletions: regional rate
variation and mechanisms of mutagenesis."
Abstract: Insertions and deletions
(indels) cause numerous genetic diseases and lead to pronounced
evolutionary differences among genomes. The macaque sequences provide an
opportunity to gain insights into the mechanism of these mutations on a
genome-wide scale by establishing the polarity of indels occurring in the
human lineage since its divergence from the chimpanzee. Here we apply
multiple regression analyses to demonstrate an extensive regional indel
rate variation stemming from local fluctuations in male and female recombination
rates, divergence, proximity to telomere, and other genomic factors. We
find that both replication and, surprisingly, recombination contribute
significantly to small indel formation. As the relative input of these
factors differs between insertions and deletions, the two types of
mutations are likely guided in part by distinct mechanisms. These results
bring us closer to unraveling the processes of indel mutagenesis.
I, Prufer K, Ji H, Zody MC, Paabo S, Ptak SE.
do human diversity levels vary at a megabase scale?
Genome Res. 2005
Speaker: SPRING BREAK - NO SEMINAR
Wadhawan -Department of Biology
Title: "Dual Coding, Duplication, Imprinting,
and Exon Shuffling Unite to Shape the Evolution of GNAS/GNAL Complex."
Abstract:Gnas and its
paralog Gnal constitute the Gs family of G-proteins that encodes the
G-protein alpha subunit. The two loci are imprinted and share significant
structural resemblance. But a unique feature distinguishing them is the
presence of functional protein-coding regions in Gnas that overlap for over
1,000 nucleotides. The two reading frames are embedded in a large
paternally transcribed (~2kb in size) upstream exon known as the XL.
Shifted one nucleotide relative to each other, the two frames when
translated code for XLαs and ALEX proteins. XLαs represents the
extra large form of the stimulatory G-protein alpha subunit. ALEX appears
to regulate signal transduction properties of XLαs by binding to
XLαs and preventing its association with receptors. The XL exon, which
encodes both proteins, evolves so rapidly that it is virtually unalignable
between primates and rodents. Even within the rodents it is highly divergent.
Despite showing so much divergence, the +1 reading frame encoding ALEX is
still preserved in these species. Here we characterize the evolution of
this exon by sequencing it in several rodents, and analyzing the sequences
together with those available for other mammals from various genome
assemblies. In addition we decipher the selection constraints acting on
other coding regions at both loci and also analyze the evolution of the Gs
Nekrutenko, A., S. Wadhawan, et al. (2005). "Oscillating evolution of
a mammalian locus with overlapping reading frames: an XLalphas/ALEX
relay." PLoS Genet 1(2): e18.
Klemke, M., R. H. Kehlenbach, et al. (2001). "Two overlapping reading
frames in a single exon encode interacting proteins--a novel way of gene
usage." Embo J 20(14): 3849-60.
Freson, K., J. Jaeken, et al. (2003). "Functional polymorphisms in the
paternally expressed XLalphas and its cofactor ALEX decrease their mutual
interaction and enhance receptor-mediated cAMP formation." Hum Mol
Genet 12(10): 1121-30.
Corradi, J. P., V. Ravyn, et al. (2005). "Alternative transcripts and
evidence of imprinting of GNAL on 18p11.2." Mol Psychiatry 10(11):
Hiroshi Akashi- Department of Biology
evolution in the Drosophila melanogaster subgroup: Lineage effects and the
time-scale of parameter fluctuations."
Abstract: Recently sequenced genomes of close relatives of Drosophila
melanogaster allow investigation of the frequency, magnitude, and genomic
breadth of parameter fluctutations in molecular evolution. In this
study, we compare patterns of codon usage and protein evolution among five
species in the D. melanogaster subgroup (D. melanogaster, simulans,
sechellia, yakuba, and erecta) for close to 10,000 genes. We employ a
maximum likelihood approach to infer ancestral states and assign
substitutions to five lineages. The magnitude of parameters governing “silent”
DNA evolution appears to have varied frequently among lineages, genomic
regions, and synonymous families. At least some of this heterogeneity
is consistent with lineage-specific selection intensity. Large-scale
changes in expression patterns may underly strong regional heterogeneity in
codon bias evolution.
(1) Akashi, H., W.Y. Ko, S. Piao, A. John, P.
Goel, C. F. Lin, and A. Vitins, 2006 Molecular evolution in the
Drosophila melanogaster species subgroup: Frequent parameter fluctuations
on the time-scale of molecular divergence. Genetics 172: 1711-1726. (2) Ko,
W. Y., S. Piao, and H. Akashi, 2006 Strong regional
heterogeneity in base composition evolution on the Drosophila X
chromosome. Genetics 174: 349-362.
Speaker: Dr. Saby
Das- Department of Biology
of Dynamic Evolution on Immunoglobulin Variable Gene Families."
Abstract: The distinction of light chain variable genes (VL)
as kappa (V ) and lambda (V ) are often confusing and their evolutionary
history is unclear. Different methods for tree building can be used but
none of them so far resolved the confusion. On the other hand, the
frequency of expansion and contraction of various heavy chain variable (VH)
gene families and their importance for the evolution of immunoglobulin
heavy chain repertoire in vertebrates is an open question. To
understand the evolutionary dynamics of VL and VH
genes we identified VL and VH sequences from several
completely sequenced vertebrate genomes. We clearly defined and distinguished
the kappa and lambda variable genes on the basis of three distinct but
conserved features. We proposed the kappa ancient hypothesis and a
model for the evolution of light chain variable genes. The ratio of the
total number of kappa and lambda chain genes varied in different lineage.
It is probably due to the differences in lineage specific expansion and/or
contraction of V or V genes. The all vertebrate VH genes can be
phylogenetically separated into eight major groups (Group A – H), in which
tetrapods are represented by three groups (groups F, G and H). There is a
biased expansion of group H genes and/or group G genes. We
hypothesized that this biased expansion can be correlated with the biased
usage of group H genes and/or group G genes and this relationship is well
conserved during evolution. There are enormous diversities in VH
gene numbers and gene orders in eutherian mammals, but the VH
locus is conserved in the subtelomeric region of the chromosome. This diversity
in number and organization of VH genes partly can be explained
by differences in evolutionary turnover of subtelomeric regions in
different species. Both VH and VL genes evolution can
be characterized by birth-and-death model. There is a significant positive
correlation between total numbers of VH and VL
families as well as between the numbers of functional genes for the
same. It supports the coevolution of VH and VL
gene families in the peculiarities of the immune systems in various
References: (1) Hsu E,
Pulham N et al (2006). “The plasticity of immunoglobulin gene systems in
evolution.” Immunol Rev 210: 8-26.
(2) Zahorsky-Reeves JL, Gregory C (2006). “Similarities in the
immunoglobulin response and VH gene usage in rhesus monkeys and humans
exposed to porcine hepatocytes.” BMC Immunol. 7: 3. (3)
Pilstrom L (2002). “ The mysterious immunoglobulin light chain.” Dev Comp
Immunol 26: 207-215. (4) Sitnikova T, Su C (1998).
“Coevolution of immunoglobulin heavy- and light chain variable region gene
families” Mol Biol Evol 15: 617-625. (5) Ota T, Nei M (1994).
“ Divergent evolution and evolution by the birth-and-death process in the
immunoglobulin VH gene family” Mol Biol Evol 11: 469-482.
Gotea- Department of Biology
Title: "The protein coding potential
of Alu elements."
elements represent a significant portion of mammalian genomes, and have
been shown to impact their functionality in several ways (Makalowski, 2000).
Of particular interest to us is their contribution to proteomes, and we
recently described cases of functional proteins that contain TE-encoded
fragments (Gotea and Makalowski, 2006). Alu elements are particularly
important to primate evolution, as they are very abundant (~1.2 million
copies in the human genome, ~10% of the genome size) and contribute with
alternatively spliced exons to many genes (Sorek et al, 2002). Here we
investigate the potential of Alu elements to encode functional protein fragments.
We also take advantage of the recently sequenced macaque genome to infer
the selection acting on Aluternative exons, and we discuss controversial
functional evidence supporting the existence of Aluternative gene variants
(Shi et al., 1999).
References: (1) Gotea, V., W.
Makalowski (2006) Do transposable elements really contribute to proteomes?
Trends in Genetics 22(5): 260-267 (2) Makalowski, W. (2000) Genomic
scrap yard: how genomes utilize all that junk. Gene 259(1-2): 61-67 (3)
Shi, B. et al. (1999) Identification and characterization of Baxe, a novel
Bax variant missing the BH2 and the transmembrane domains. Biochemical and
Biophysical Research Communications 254: 779-785 (4) Sorek, R., G.
Ast, D. Graur (2002) Alu-containing exons are alternatively spliced. Genoem
Research 12: 1060-1067
Li- Department of Biology
Title: "Global Regulation of
Gene Expression in Guard Cells."
Abstract: Guard cells (GC) have
been long studied for elucidation of ABA signal transduction using
electrophysiological, biochemical and molecular genetic methods. Here we
take a genomics approach to study the transcriptome of GC. We have
established methods to obtain pure GC RNA with or without ABA treatment and
have used these samples to hybridize whole genome Affymetrix chips (ATH1).
Leaf (LF) RNA samples with or without ABA were also used to hybridize to
ATH1 chips in parallel.
Gene expression in higher eukaryotes is a
complex process and is under integrated control of both developmental and
environmental cues. We study developmental control by looking at tissue
specific gene expression profiles of Arabidopsis guard cells (GC)
versus leaves (LF), and we study environmental control by comparing gene
expression in the two tissues in response to the stress hormone, abscisic
We use the gene expression profiles
generated from our lab, and integrate other publicly available
computational and experimental resources, to study four putative regulatory
mechanisms that are likely to be involved in transcriptional regulation in
GC and LF. The four mechanisms we look at are cis-regulatory element
regulated gene expression, co-expression clusters on chromosomes, microRNA
regulated gene expression and cis-antisense regulated gene expression. We
finally evaluate the relative importance of four regulatory mechanisms
using a log likelihood score (LLS).
Sona Pandey*, Song Li*, Zhixin Zhao*, Laetitia Perfus*,
Liza Wilson*, Timothy Gookin*, and Sarah M. Assmann*
Penn State University.
This reference not yet published.
Duarte- Department of Biology
Title: "Identification of conserved single copy nuclear
genes in Arabidopsis, Populus, and rice and their phylogenetic utility."
Duarte, J. M., Wall, P. K., Beckmann, K., Landherr, L. L., Leebens-Mack, J.
H., dePamphilis, C. W.
Abstract: Although the overwhelming majority of genes found
in angiosperms are members of gene families, we have identified a series of
genes that are conserved as single copy genes in the Arabidopsis, Populus,
and rice genomes. To characterize these genes, we have performed a number
of analyses examining GO annotations, cDNA length, number of exons,
expression patterns, and presence in the Selaginella and Physcomitrella
genomes. There are 1574 single copy nuclear genes conserved in
Arabidopsis and rice; 727 single copy genes conserved in Arabidopsis,
Populus, and rice; and the majority of these genes are also present in the
Selaginella and Physcomitrella draft genomes. The selective forces leading
to continuous loss of duplicated genes for some kinds of genes and not
others are still unknown, but the collection of genes is biased toward
organellar genes and genes of unknown biological function. Public EST
sets for 41 species suggest that most of these genes are conserved as
single or very low copy genes, though exceptions are seen especially in
very recent polyploidy taxa. In order to explore the phylogenetic utility
of a number of these genes we have performed a series of phylogenetic
analyses using publicly available ESTs. Conserved single copy nuclear genes
provide a vast source of new evidence for plant phylogeny, genome mapping,
and other applications.
Mort, M.-E., and D. J. Crawford. 2004. The continuing
search: low-copy nuclear sequences for lower-level plant molecular
phylogenetic studies. Taxon 53:257-261.
Sang, T. 2002. Utility of low-copy nuclear gene
sequences in plant phylogenetics. Critical Reviews in Biochemistry and Molecular
Small, R. L.,
R. C. Cronn, and J. F. Wendel. 2004. Use of nuclear genes for phylogeny reconstruction
in plants. Australian Systematic Botany 17:145-170.
Chalkia- Department of Biology
Analysis of Formin Genes in Eukaryotes and Inference of their Functional
Abstract: One of the most interesting
properties of the eukaryotic cell is the ability to change its shape and
activity rapidly in response to internal and external signals. This
property comes from the cell’s ability to remodel the actin and microtubule
cytoskeletons with appropriate timing and precision. Recently, formin has
emerged as a key molecular regulator of the eukaryotic cytoskeletal
assembly and organization. Formin is a large multidomain protein that is
expressed widely in mammalian cells. This dynamic molecule associates with
a variety of other cellular factors and assembles actin filaments through a
novel migratory mechanism. In this study we have shown that formin genes
exist in all eukaryotic genomes while bacterial and archaeal genomes are
devoid of formin or formin-like genes. Our phylogenetic analysis, based on
formin’s most conserved module (FH2 module), suggests that multiple events
of expansion and contraction of copy number have occurred in this gene
family. Of special interest is the birth of all metazoan formin gene groups
before the emergence of multicellular organisms. Unicellular organisms that
form colonies under certain conditions (e.g., Monosiga brevicollis
and Dictyostellium discoideum) have multiple copies of formin genes,
which are orthologous to most animal formin genes. The pattern of modular
architecture of eukaryotic formin proteins can be classified according to
the phylogenetic clustering. The conservation of the functionally important
residues in all formins implies that the core function of the FH2 domain,
i.e. polymerization and assembly of actin filaments is conserved. Our data
suggest that the high degree of divergence of different groups of formin
molecules is a product of mutations that evolved in a more or less neutral
fashion. We speculate that neutral mutations coupled with the
insertion/deletion of specific modules provided the means for temporal
and/or spatial differentiation of gene function and thus led to the
evolution of a highly coordinated cytoskeletal regulatory system.
HN (2005) Formin proteins: a domain based approach. Trends Biochem. Sci.
30(6):342-353.Goode BL and Eck MJ (2007) Mechanism and function of formins
in the control of actin assembly. Ann. Rev. Biochem 76:32.1-32.35.