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Topic Name: Biological Significance Of Modular Structures In Protein Networks
Category: Genetic Engineering
Research persons: Jianzhi Zhang & Jianzhi Zhang
Location: 2019 Kraus Natural Science Building,830 North University,Ann Arbor, MI 48109-1048,p: 734.615.4917 // f: 734.763.0544, United States
Details
It is easy to observe that many networks naturally divide into communities or
modules, where links within modules are stronger and denser than those across
modules - like the way people from the same age group tend to interact more with
each other than with people from different age groups. It is widely believed
that networks within cells are modular in much the same way. Drs Zhi Wang and
Jianzhi Zhang, from the University of Michigan, now investigate these modular
properties and conclude that they may be only a random byproduct of evolution,
and not functional at all.
The modules of cellular networks were thought to be formed in a way that
reflects the relative independence and coherence of the various functional units
in a cell - each module serves a function. This investigation, published in the
Open Access journal PLoS Computational Biology, now suggests that the
structural modules in the yeast protein-protein interaction network may have
originated as an evolutionary byproduct without much biological significance.
There is little evidence that the previously observed structural modules
correspond in any way to functional units. It seems that previous analyses may
have even created some of these modules through the techniques used to
investigate protein properties. Refuting previous studies, the authors now show
by computer simulation that modular structures can arise during network growth
via a simple model of gene duplication, without a natural selection preference
for modularity.
Author Summary
Many complex networks are naturally divided into communities or modules,
where links within modules are much denser than those across modules. For
example, human individuals belonging to the same ethnic groups interact more
than those from different ethnic groups. Cellular functions are also organized
in a highly modular manner, where each module is a discrete object composed of
a group of tightly linked components and performs a relatively independent
task. It is interesting to ask whether this modularity in cellular function
arises from modularity in molecular interaction networks such as the
transcriptional regulatory network and protein–protein interaction (PPI)
network. We analyze the yeast PPI network and show that it is indeed
significantly more modular than randomly rewired networks. However, we find
little evidence that the structural modules correspond to functional units. We
also fail to observe any evolutionary conservation among yeast, fly, and
nematode PPI modules. We then show by computer simulation that modular
structures can arise during network growth via a simple model of gene
duplication, without natural selection for modularity. Thus, it appears that
the structural modules in the PPI network may have originated as an
evolutionary byproduct without much biological significance.
About Researchers:
Jianzhi Zhang & Jianzhi Zhang
Department of Ecology and Evolutionary Biology,
University of Michigan,
Ann Arbor,
Michigan,
United States of America
Funded-
This work was
supported in part by research grants from the US National Institutes of Health
and the University of Michigan to
JZ.
In The Images-
Figure
1. An Example of a Small Network with a Modular Structure (A) and
Its Randomly Rewired Network (B)
Figure
2. The Modularity of Yeast PIC and PEC Networks Compared with That
of Their Randomly Rewired Networks, and the Similarity of Module Compositions
between PIC and PEC Networks Compared with the Random Expectatio
Figure
3. PPI Network Representations of Protein Complexes
Figure
4. Lack of Obvious Correspondence between Structural Modules and
Functional Units
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