The metabolic network can be discussed at different levels: genome (DNA level), metabolic pathway and biochemical reaction network (protein level), metabolic flow (logistics level), metabolic physiology (microbial cell level), etc.For the metabolic network at the protein level, a metabolite molecule is a node, and the connection between nodes is a biochemical reaction.Most molecules only participate in one or two reactions, but a few molecules participate in many reactions. They are actually the distribution center or current metabolites of metabolic streams.
(1) CellularMetabolic networkIt is a scale-free network in the biological world
"Net" originally refers to a porous fishing or animal catching apparatus formed by alternately tying a group of lines (or ropes) into knots ("knots"). The "knots" of the lines on the net are equivalent to "nodes" in the network structure.The natural network structure is mostly random, while the artificial network structure is mostly regular.In a random network structure, the number of connections between nodes and other nodes is normally distributed;In a regular network structure, the number of connections between nodes and other nodes is fixed.In the above two types of networks, the number distribution of connections between nodes and other nodes has rules to follow, so they are scaled networks.However, when describing the Internet with mathematical methods, it is unexpectedly found that some nodes are connected with a large number of other nodes, forming a collection and distribution center (called a collection and distribution node). Therefore, a network such as the Internet is called a scale-free network.
The scale-free network contains countless nodes, most of which have only a few connections with other nodes. Some nodes connect with a large number of other nodes, which are called collector distributor nodes.The scale-free network does not have representative nodes, but is dominated by a small number of collector distributor nodes, and has the following predictable behavior characteristics: it has an amazing tolerance for unexpected events, is vulnerable to coordinated attacks, and is subject to some basic laws.
Based on the above analysis, the metabolic network of cells is a scale-free network in the biological world.
Different levels
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(2) Metabolic networks at different levels
From low level to high level, and from large platform to small platform, corresponding level by level activation is required.Some genes in the genome are activated and expressed, forming metabolic pathways and biochemical reaction networks;At any time, the metabolic flow only flows in the local or some pathways of the biochemical reaction network;Only a part of metabolic flow contributes to the emergence of some physiological state of microbial cells.
origin-destination
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(3) The metabolic network has no absolute starting point and end point, and the metabolic pathway, as a metabolic channel, has starting and ending points
For the continued microbial life, there is no absolute starting point or end point for the metabolic network, forming four reaction groups (productivity reaction group, biosynthesis reaction group, poly reaction group, assembly reaction group) of cells, and the three major plates of primary metabolism (centripetal plate, central plate, centrifugal plate) are connected in two to form a whole.
The metabolic network of microorganisms is like the railway bureaus and railway transportation networks composed of many railway lines.When we use the specified raw materials to produce a specific fermentation product, we expect the organic material to claim the fermentation product through the path most conducive to high yield (ideal flow carrying path);Just as we have to choose a suitable railway line when we go to a city by train.The national railway network is divided into several railway administration areas, which is equivalent to that the metabolic network is divided into three sections;The railway line can cross the railway bureau, which is equivalent to that the current carrying path can cross the network plate.The working mode of the microbial cell machine describes the current carrying path in the running stage of the cell machine as a "channel" connecting the centripetal path, central path and centrifugal path in turn.
environmental effect
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(4) The metabolic network has always been in response to changes in the environment
In fact, the metabolic network of microbial cells has always been in response to changes in the environment, so the concept of metabolic network is a virtual network concept.The terminal of the centrifugal path in the network may become the starting point of the centripetal path;There is more than one central path in the network, and there are branches. There are also many centripetal paths and centrifugal paths, and there are also convergence or branches.There may also be horizontal links between pathways (including the balance of reducing power and metabolic energy).The extension of metabolic pathways (such as secondary metabolic pathways) when growth stops, and the selective separation of various metabolic factors in different cell spaces, make the metabolic network more complex.Because human beings do not fully understand metabolism, their understanding of metabolic network is only relative, and their understanding of metabolism needs to be deepened.The gradual improvement and development of the metabolic network hypothesis can illustrate this point.
