Alu sequences and human evolution

FOSTERCMD fostercmd at aol.com
Thu Jul 21 04:30:05 EST 1994


Subj:	ALU SEQUENCES and human evolution
Date:	94-07-20 07:48:40 EDT
From:	haross at students.wisc.edu
To:	FOSTERCMD

MESSAGE OF 1 OF 2

 Here is some info on Alu represents and human evolution. The second part
of 
this message provides information on viral taxonomy. 
 Alu repeats result from RNA that has been reversely transcribed back into

the DNA. There are hundreds of thousands of sequences and they make up
about 
5% of the total DNA. The full sequence is about 200 nucleotides long and 
very closely resembles 7SL RNA. This RNA binds with 6 proteins to form the

signal recognition particle (SRP). When a new protein is being synthesized

the SRP binds the nascent protein chain, halting synthesis until the SRP
can 
bind to an endoplasmic reticulum (ER) channel protein (Sec61p). This
allows 
the ribosome to bind to the ER and the nascent protein to translocate into

the ER.
 Whether the reverse transcriptase arose via mutation, viral  infection or

some other means is not known.
 Hope these shed some  light.

 ALU AND EVOLUTION

1.
Authors
  Shen MR.  Batzer MA.  Deininger PL.
Title
  Evolution of the master Alu gene(s).
Source
  Journal of Molecular Evolution.  33(4):311-20, 1991 Oct.
Abstract
  A comparison of Alu sequences that comprise more recently amplified Alu
  subfamilies was made. There are 18 individual diagnostic mutations
  associated with the different subfamilies. This analysis confirmed that
  the formation of each subfamily can be explained by the sequential
  accumulation of mutations relative to the previous subfamily. Polymerase
  chain reaction amplification of orthologous loci in several primate
  species allowed us to determine the time of insertion of Alu sequences
in
  individual loci. These data suggest that the vast majority of Alu
elements
  amplified at any given time comprised a single Alu subfamily. We find
  that, although the individual divergence relative to a consensus
sequence
  correlate reasonably well with sequence age, the diagnostic mutations
are
  a more accurate measure of the age of any individual Alu family member.
  Our data are consistent with a model in which all Alu family members
have
  been made from a single master gene or from a series of sequential
master
  genes. This master gene(s) accumulated diagnostic base changes,
resulting
  in the amplification of different subfamilies from the master gene at
  different times in primate evolution. The changes in the master gene(s)
  probably occurred individually, but their appearance is clearly
  punctuated. Ten of them have occurred within an approximately
  15-million-year time span, 40-25 million years ago, and 8 changes have
  occurred within the last 5 million years. Surprisingly, no changes
  appeared in the 20 million years separating these periods.

2.
Authors
  Gonzalez IL.  Tugendreich S.  Hieter P.  Sylvester JE.
Title
  Fixation times of retroposons in the ribosomal DNA spacer of human and
  other primates.
Source
  Genomics.  18(1):29-36, 1993 Oct.
Abstract
  We have investigated the presence/absence of two types of retroposed
  sequences found in human ribosomal DNA in equivalent positions in
  chimpanzee, gorilla, orangutan, gibbon, and rhesus monkey rDNA. These
  sequences are one pseudogene derived from the single-copy cdc27hs gene
and
  seven complete Alu elements. The 2-kb pseudogene is present in the apes
  but not in Old World monkeys, indicating fixation in an ape ancestor.
Five
  of the Alu elements are shared by the whole set of primates studied,
  indicating insertion and fixation prior to the split of the ape and Old
  World monkey lineages. One is absent only from the rhesus monkey rDNA,
and
  another is absent from both gibbon and rhesus rDNA, indicating fixation
at
  different times in primate evolutionary history. Since branching times
for
  the primate phylogenetic tree are known from a combination of the fossil
  record and multiple molecular data sets, it is possible to compare Alu
  fixation times determined from the phylogenetic information with those
  calculated from Alu element mutation rates.

3.
Authors
  Chang DY.  Maraia RJ.
Title
  A cellular protein binds B1 and Alu small cytoplasmic RNAs in vitro.
Source
  Journal of Biological Chemistry.  268(9):6423-8, 1993 Mar 25.
Abstract
  B1 and Alu are sequence-homologous interspersed elements of unknown
  function that have expanded in the genomes of mice and humans,
  respectively. A minority of B1 and Alu sequences are expressed as small
  cytoplasmic RNAs. These RNAs have conserved a secondary structure motif
  also present in signal recognition particle (SRP) RNA despite
substantial
  sequence divergence, whereas random B1 and Alu sequences have not. This
  RNA structure has also been conserved by the source sequences that gave
  rise to successive transpositions during B1 and Alu evolution. In the
  present work small cytoplasmic B1 and Alu RNAs synthesized in vitro were
  found to bind a cellular protein by mobility shift and UV cross-linking
  analyses. The mouse and human proteins demonstrate the same specificity
to
  a panel of competitor RNAs. Results using mutated B1 RNA indicate that a
  single strand loop in the conserved Alu motif is essential for binding.
  Previous work by Strub et al. (Stub, K., Moss, J. B., and Walter, P.
  (1991) Mol. Cell. Biol. 11, 3949-3959) demonstrated that the
Alu-specific
  protein SRP 9/14 does not footprint to this region of SRP RNA. This
  observation coupled with the failure of anti-SRP/9 antibodies to
identify
  SRP 9/14 in the B1 RNA-protein complex as well as the apparent mass and
  other characteristics of the protein described here suggest that it is a
  novel B1-Alu RNA-binding protein. Conservation of primary and secondary
  structure by B1 and Alu small cytoplasmic RNAs as well as features of
  their specific expression and ability to interact with the conserved
  binding protein indicate that these RNAs are more homologous than
  previously appreciated.

4.
Authors
  Hellmann-Blumberg U.  Hintz MF.  Gatewood JM.  Schmid CW.
Institution
  Department of Chemistry, University of California, Davis 95616.
Title
  Developmental differences in methylation of human Alu repeats.
Source
  Molecular & Cellular Biology.  13(8):4523-30, 1993 Aug.
Abstract
  Alu repeats are especially rich in CpG dinucleotides, the principal
target
  sites for DNA methylation in eukaryotes. The methylation state of Alus
in
  different human tissues is investigated by simple, direct genomic blot
  analysis exploiting recent theoretical and practical advances concerning
  Alu sequence evolution. Whereas Alus are almost completely methylated in
  somatic tissues such as spleen, they are hypomethylated in the male germ
  line and tissues which depend on the differential expression of the
  paternal genome complement for development. In particular, we have
  identified a subset enriched in young Alus whose CpGs appear to be
almost
  completely unmethylated in sperm DNA. The existence of this subset
  potentially explains the conservation of CpG dinucleotides in active Alu
  source genes. These profound, sequence-specific developmental changes in
  the methylation state of Alu repeats suggest a function for Alu
sequences
  at the DNA level, such as a role in genomic imprinting.

5.
Authors
  Minghetti PP.  Dugaiczyk A.
Title
  The emergence of new DNA repeats and the divergence of primates.
Source
  Proceedings of the National Academy of Sciences of the United States of
  America.  90(5):1872-6, 1993 Mar 1.
Abstract
  We have identified four genetic novelties that are fixed in specific
  primate lineages and hence can serve as phylogenetic time markers. One
Alu
  DNA repeat is present in the human lineage but is absent from the great
  apes. Another Alu DNA repeat is present in the gorilla lineage but is
  absent from the human, chimpanzee, and orangutan. A progenitor Xba1
  element is present in the human, chimpanzee, gorilla, and orangutan, but
  only in the human lineage did it give rise to a transposed progeny,
Xba2.
  The saltatory appearance of Xba2 is an example of a one-time event in
the
  evolutionary history of a species. The enolase pseudogene, known to be
  present as a single copy in the human, was found to be present in four
  other primates, including the baboon, an Old World monkey. Using the
  accepted value of 5 x 10(-9) nucleotide substitutions per site per year
as
  the evolutionary rate for pseudogenes, we calculated that the enolase
  pseudogene arose approximately 14 million years ago. The calculated age
  for this pseudogene and its presence in the baboon are incongruent with
  each other, since Old World monkeys are considered to have diverged from
  the hominid lineage some 30 million years ago. Thus the rate of
evolution
  in the enolase pseudogene is only about 2.5 x 10(-9) substitutions per
  site per year, or half the rate in other pseudogenes. It is concluded
that
  rates of substitution vary between species, even for similar DNA
elements
  such as pseudogenes. We submit that new DNA repeats arise in the genomes
  of species in irreversible and punctuated events and hence can be used
as
  molecular time markers to decipher phylogenies.

6.
Authors
  Quentin Y.
Institution
  Theoretical Biology and Biophysics Group, Los Alamos National
Laboratory,
  NM 87545.
Title
  Origin of the Alu family: a family of Alu-like monomers gave birth to
the
  left and the right arms of the Alu elements.
Source
  Nucleic Acids Research.  20(13):3397-401, 1992 Jul 11.
Abstract
  The Alu dimeric elements are a common feature of the primate genomes,
  where they constitute a family of related sequences (1). The
  identification of a free left Alu monomer (FLAM) family plus a free
right
  Alu monomer (FRAM) family suggests that the dimeric structure results
from
  the fusion of a FLAM sequence with a FRAM sequence (2). Here, we
describe
  a very old Alu-like monomeric family, referred to as FAM for fossil Alu
  monomer. This family arose from a 7SL RNA sequence and gave birth to the
  FLAM and FRAM families. From the results obtained, the evolution of the
  Alu family can be subdivided into two phases. The first phase, which
  involves only monomeric elements, is characterized by deep remodelling
of
  the progenitor sequences and ends with the appearance of the first Alu
  dimeric element through the fusion of a FLAM and a FRAM element. The
  second phase, still in progress, starts with the first Alu dimeric
  element. This phase is characterized by the stabilization of the
  progenitor sequences.

7.
Authors
  Liu WM.  Leeflang EP.  Schmid CW.
Title
  Unusual sequences of two old, inactive human Alu repeats.
Source
  Biochimica et Biophysica Acta.  1132(3):306-8, 1992 Oct 20.
Abstract
  Two human Alu repeats terminating in an oligo(T) run rather than the
usual
  A-rich 3' tail were isolated by library screening. Base sequence
  comparisons reveal that these unusual Alus are also exceptionally
  divergent from other Alu family members implying that they are
  evolutionarily old. Unlike other members of the family, they are not
  transcribed in vitro by RNA polymerase III (Pol III) suggesting a
partial
  explanation for how Alu source genes might become inactive with age.
Hugh Ross
78 Craig Avenue
Madison, Wisconsin 53705
608-231-6828
fax 608-231-6769





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