March 21st, 2006

homuncul

БИОЛОГИЯ

Есть ли феномен адаптивных мутаций? - пока вопрос открыт..


Annual Review of Genetics, Dec. 1999
MECHANISMS OF STATIONARY PHASE MUTATION: A Decade of Adaptive Mutation

A decade of research on adaptive mutation has revealed a plethora of mutagenic mechanisms that may be important in evolution. The DNA synthesis associated with recombination could be an important source of spontaneous mutation in cells that are not proliferating. The movement of insertion elements can be responsive to environmental conditions. Insertion elements not only activate and inactivate genes, they also provide sequence homology that allows large-scale genomic rearrangements. Some conjugative plasmids can recombine with their host's chromosome, and may acquire chromosomal genes that could then spread through the population and even to other species. Finally, a subpopulation of transient hypermutators could be a source of multiple variant alleles, providing a mechanism for rapid evolution under adverse conditions


Nature Reviews Genetics (2001)
EVOLVING RESPONSIVELY: ADAPTIVE MUTATION

A basic principle of genetics is that the likelihood that a particular mutation occurs is independent of its phenotypic consequences. The concept of adaptive mutation seemed to challenge this principle with the discoveries of mutations stimulated by stress, some of which allow adaptation to the stress. The emerging mechanisms of adaptive genetic change cast evolution, development and heredity into a new perspective, indicating new models for the genetic changes that fuel these processes.


MOLECULAR STRATEGIES IN BIOLOGICAL EVOLUTION
Annals of the New York Academy of Sciences, May 1999
http://www.annalsnyas.org/content/vol870/issue1/
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homuncul

БИОЛОГИЯ

про эпигенетическое наследование...

Nature, January 2003
Controlling the double helix

Chromatin is the complex of DNA and proteins in which the genetic material is packaged inside the cells of organisms with nuclei. Chromatin structure is dynamic and exerts profound control over gene expression and other fundamental cellular processes. Changes in its structure can be inherited by the next generation, independent of the DNA sequence itself.
homuncul

ЭВОЛЮЦИЯ

Расшифровка все большего числа геномов микроорганизмов меняет представления о механизмах ранней эволюции. Если традиционно филогения представлялась в виде дерева, потом в виде куста, то теперь она все больше напоминает сеть. Причина тому горизонтальный перенос генов (HGT), который особенно интенсивен в мире прокариот, и является у них столь же распространенным способом передачи наследственного материала, как и вертикальное наследование (предок-потомок).
В результате прежние схемы, строившиеся без учета роли HGT, не отражают реальной картины эволюционных процессов. Показатели гомологии генов традиционно трактовались как степень родства, тогда как во многих случаях это может быть результатом горизонтального переноса, что, соответственно, радикально меняет всю схему "отношений" между видами.
Авторы "Prokaryotic Evolution in Light of Gene Transfer" показывают, как молекулярные данные могут вводить в заблуждение:

Gene transfer can create patterns of similarity and difference that mimic patterns produced by vertical descent. If taxa A and B successfully exchange genetic information (by homologous recombination or HGT) more frequently with each other than with taxon C, they will come to resemble each other more closely than they do C, both in gene content and gene sequence. Treelike patterns based on gene content or sequence will reflect these different frequencies, not some underlying organismal phylogeny.
Deep branching (as of taxon C) may reflect genetic isolation, not early divergence. Conversely, "distantly related" taxa that begin to exchange genes very frequently will ultimately resemble "sister" taxa.

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traditional models for prokaryotic evolution based on clonality and periodic selection are inadequate to describe the process of prokaryotic evolution at the species level and that treelike phylogenies are inadequate to represent the pattern of prokaryotic evolution at any level.
Here we elaborate on this new understanding to show that a coherent model for prokaryotic evolution which invokes gene transfer as its principle explanatory force is feasible and would have many benefits for understanding diversification and adaptation.



- HGT can fundamentally alter the character of a microbial species by introducing fully functional genes and gene clusters that can confer complex phenotypes and functions. In contrast, variation introduced by point mutation will, most of the time, only adjust preexisting phenotypes.

- While fitness peaks may never be explored if they must be reached one gene at a time, multiple genes may be acquired in the form of bacterial operons and gene clusters.

- No gene appears immune to HGT. Genes encoding core metabolic functions..., conserved biosynthetic pathways..., components of the transcription and translation machinery..., and even ribosomal RNA... have been subject to HGT.

- Ironically, ...preferential gene exchange could create many of the very same patterns of similarity and difference we usually attribute to vertical inheritance. Only a small subset of HGTs can be detected with confidence; the majority of transfers, especially those that occurred long ago or between closely related species, will likely escape detection.

- The mismatch repair genes themselves show a complex history of recombination attributed to loss and recovery (through horizontal transfer).... Embracing gene transfer promises a broad and radical revision of the prokaryotic evolutionary paradigm. HGT can occur between even very distantly related organisms, e.g., between bacteria and plants or fungi....



Molecular Biology and Evolution, Dec. 2002
Prokaryotic Evolution in Light of Gene Transfer
homuncul

ЭВОЛЮЦИЯ

В продолжение темы ранней эволюции...Проведена попытка по расшифрованным геномам восстановить общий вид "сети".

Since the time of Darwin, the evolutionary relationships between organisms have been represented as a tree, with the common ancestors at the base of the trunk and the most recently evolved species at the tips of the branches. Microbiologists have argued for a long time that this representation doesn't really hold true for microbes, which often exchange genes among different species. Their claim has been that the evolution of these organisms is better represented by a net. Unfortunately, no-one knew exactly where to draw the horizontal lines in this net.

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Victor Kunin, previously a PhD student in Christos Ouzounis's group, and their colleagues have now constructed a map of microbial evolution, going back billions of years to the last universal common ancestor, that includes these horizontal lines. "Reassuringly, evolutionary trees constructed by many independent methods and different research groups are remarkably consistent with each other, projecting the same story. We used these trees as the scaffold of the net, on which we looked for the evidence of horizontally transferred genes," explains Victor.

http://www.embl.org/aboutus/news/press/2005/press1jul05.html


Genome Research, July 2005
The net of life: Reconstructing the microbial phylogenetic network