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2\14 Studies examine evolution of two world-altering chemical processes in
biosphere, point to possible origin
Part 1 of 2

Arizona State University
Tempe, Arizona

Contact:
James Hathaway, jim.hathaway{at}asu.edu, (480) 965-6375 

February 14, 2003

Studies examine evolution of two world-altering chemical
    processes in biosphere, point to possible origin
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Some of the most important evolutionary events in Earth's history 
didn't just create new organisms -- they created new fundamental 
biochemical processes. And where do biochemical processes come from? 
They evolve from other biochemical processes.

Two of the most important pieces of biochemical innovation that 
occurred in the early biosphere -- the development of photosynthesis 
(which made light energy available to life) and of nitrogen fixation 
(which made atmospheric nitrogen available to life) -- may be related 
to each other because some of their key enzymes appear to have evolved 
from a common ancestor that may be part of a third, significantly
different, biochemical process.

"Photosynthesis was important because it gave life an enormous energy 
source and ultimately put oxygen in the atmosphere," said Arizona 
State University biochemist Robert Blankenship. "Nitrogen fixation -- 
making atmospheric nitrogen bioavailable -- was also a critical step 
in the early development of life. We need a good source of nitrogen 
for proteins and DNA, but the biggest source, the molecular nitrogen 
that we have in the atmosphere, has a triple bond in it that makes it 
so inert that it's a killer to get at."

Two new studies, to be presented at the February 2003 NASA 
Astrobiology Institute General Meeting by researchers at Arizona State 
University, provide evidence for the long-suspected relatedness of the 
two biochemical pathways, and find hints of other related pathways 
that may be key to understanding the evolutionary history of both. A 
critical part of the emerging evolutionary picture seems to be 
"horizontal gene transfer" -- genetic change that occurs by the 
exchange of genetic material between bacteria. This process allows for 
sudden evolutionary leaps that are perhaps not possible through
gradual genetic change and natural selection. 

In a paper published in the November 22, 2002 issue of Science, 
Blankenship, ASU biochemist Jason Raymond and colleagues show through 
a comparative genomic analysis of five photosynthetic prokaryotic 
organisms that the genes that code for the intricate molecular 
complexes that perform photosynthesis seem to have originated through 
ancient genetic mixing that apparently combined a variety of 
independently evolved metabolic processes. 

In one of the Astrobiology meeting papers, "Horizontal Gene Transfer 
in the Evolution of Nitrogen Fixation," Raymond, Blankenship and Rice 
University's Janet Siefert do an analysis of the genomes of a larger 
group of bacteria and archaea, comparing in particular similar genes 
that code for the protein nitrogenase, a critical enzyme in nitrogen 
fixation. 

"In the very early earth, there was probably some available nitrogen 
in the form of ammonia or something else, so early life forms didn't 
have to fix nitrogen from the atmosphere. At some point though, things
reached a food crisis -- you either find someway to get the 
atmosphere's molecular nitrogen into the cycle or you die. A minimum 
input of nitrogen can't sustain a big biosphere," noted Blankenship.

"Nitrogen fixation is one of the most interesting biological processes 
because it's so difficult to do chemically. Nitrogenase is a very 
complex enzyme system that actually breaks molecular nitrogen's triple 
bond," he said.

The researchers find that similar or "homologous" nitrogenase genes 
exist across a broad range of organisms, and appear to be related to 
other similar genes coding for proteins involved in photosynthesis, as 
well as to other genes in archaea and bacteria that do neither 
photosynthesis nor nitrogen fixation. 

"We found a group of homologous genes that doesn't correspond to any 
genes that go with photosynthesis or any that we know in nitrogen 
fixation -- we found these in a wide range of organisms," said 
Raymond.

The analysis suggests that the related genes that code for neither 
nitrogenase nor enzymes in photosynthesis may be "relics," coding for 
metabolic pathways that are ancestral to both photosynthesis and 
nitrogen fixation. Horizontal gene transfer appears to be responsible 
for the broad distribution of the original gene and for its subsequent 
divergence and specialization in the metabolic pathways of nitrogen 
fixation and photosynthesis.

In the second paper, "The Evolutionary Relationship between Nitrogen 
Fixation and Bacteriochlorophyll Synthesis," ASU's Christopher 
Staples, Blankenship, and Virginia Polytechnic Institute's Biswarup
Mukhopadhyay examine the properties of enzymes created by these 
similar genes and finds that nitrogenase, the photosynthesis related 
enzymes, and other homologous enzymes all generally belong to a group 
of enzymes that break apart molecules and are known as reductase 
enzymes.

"We're purifying the proteins that the genes produce and will be 
looking at catalytic activity. We will test to see how activity 
differs and also to find what has been conserved and what has been 
changed in the active sites," said Staples. "Changes in the enzymes' 
active sites lead to differentiation in regard to what specific 
molecules they affect."

The less-specialized reductase enzymes appear to be ancestral to the 
others and were perhaps originally important in helping early 
prokaryotes neutralize toxic substances in their environment.

"There is a hypothesis that the ancient reductase, in the presence of 
a reducing atmosphere, may have been a hydrogen cyanide reductase," 
said Staples.

The team thinks that they have perhaps found a living model for this 
in Methanococcus jannaschii, a methane- producing archaea that 
performs neither nitrogen fixation nor photosynthesis but produces a 
reductase enzyme that the researchers suspect is used to break down 
hydrogen cyanide. 

"We're testing to see if these organisms can grow in the presence of 
cyanide and if they can use cyanide as a nitrogen source," said 
Staples. "They don't appear to be able to use cyanide exclusively for
nitrogen, but they can grow in concentrations of it that would be 
deadly to most organisms."

While the search to discover the evolutionary history of the key 
chemical processes of the biosphere involves some esoteric genomic and 
biochemical detective work, Blankenship, Raymond and Staples point out 
that understanding how the chemical processes of photosynthesis and 
nitrogen fixation evolved may have some large practical pay-offs.

"Understanding the origins of nitrogenase, for example, links to 
things like the synthesis of fertilizer," said Blankenship. "I come 
from the Midwest where there are these huge anhydrous ammonia plants 
that are tremendous users of energy -- a fantastic amount of energy 
goes into the making of ammonia. But that's exactly what this enzyme 
complex does: make ammonia out of nitrogen.  It's a bio solution to 
this incredibly important and very expensive process of fertilizer 
production.

(continued)

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