I've found
LUCApedia -- from
its about page,
Thanks to the growth of genomics, proteomics, and metabolomics, it is possible to investigate properties of the Last Universal Common Ancestor (LUCA) and its predecessors in detail. LUCApedia was established to aggregate and unify the results of studies aimed at describing early life through a variety of bioinformatics approaches and pair them with a number of enzymological characteristics predicted in previous studies to reflect catalysts important in the early evolution of life. Users may query the webserver for individual proteins to rapidly identify evidence of deep ancestry. Advanced users may download the database as a series of flat files and use it to discover trends in early enzymatic and metabolic evolution and to test hypotheses related to early life.
I'd like a nontechnical summary of what this database is for, and some discoveries made with its data. But that page does link to some interesting work.
In the middle of the page is a list of kinds of cofactors, small molecules and sometimes ions that work with the protein parts of enzymes, either free-floating or attached. The B vitamins are all cofactors. There are several types:
- Derived from nucleotides -- likely a leftover from the RNA world
- Derived from amino acids
- Iron-sulfur
- Zinc
The Genetic Core of the Universal Ancestor
Our analyses identified a small set of genes that can be traced back to the universal ancestor and have coevolved since that time. As indicated by earlier studies, almost all of these genes are involved with the transfer of genetic information, and most of them directly interact with the ribosome. Other universal genes have either undergone lateral transfer in the past, or have diverged so much in sequence that their distant past could not be resolved.
Their method: by looking for proteins whose phylogenies parallel the ribosomal-RNA phylogeny, as a way of excluding lateral gene transfer. That is very common in metabolism-related genes.
Here are the main groups of what they found:
Group 1: Ribosomal Proteins and Translation Initiation Factors
Group 2: Proteins Associated With the Ribosome or Protein Modification
Group 3: Proteins Associated With Transcription and Replication of DNA
Group 4: Uncharacterized Proteins
The Canonical Network of Autotrophic Intermediary Metabolism: Minimal Metabolome of a Reductive Chemoautotroph
and a successor paper,
Analysis of the Intermediary Metabolism of a Reductive Chemoautotroph
From the first one,
The reductive Krebs cycle is the starting point for both amino acids and nucleotides, and these are in turn a starting point for several cofactors.
Typical examples are CoA, that has an AMP handle bridged through pantothenic acid to a modified (decarboxylated) cysteine and S-adenosyl-l-methionine (SAM) which is a direct chimera of ATP and methionine. In addition to CoA and SAM, many other cofactors like NAD, NADP, FAD, and ATP are all nucleotides or contain heterocyclic nitrogenous bases as seen in thiamin diphosphate (ThPP) and tetrahydrofolate (THF).
Many of the chemical mechanisms involved in biosynthesis fall into a few basic categories, each with its own sort of cofactors:
These reactions include (i) oxidation-reduction, (ii) carboxylation-decarboxylation, (iii) hydrolysis-dehydration, (iv) phosphorylation-dephosphorylation, (v) amination, and (vi) acylation; all these reactions are enabled by specific cofactors in enzyme-catalyzed transformations.
From the second one:
A diagram of amino-acid and nucleotide biosynthesis -- rather complicated, but it shows how few starting points it has.
The authors have several generalizations:
#1. C, H, N, O, P, S -- the universal components. The first four are the most widely-used of them. Their smallness enables forming stable chemical bonds. Si-Si isn't as good as C-C, something that counts against silicon-based biochemistry. Sulfur makes weaker bonds, something that is sometimes convenient. Phosphorus appears as phosphates, and they also make weaker bonds.
The authors didn't address the question of why halogens are rare in biological molecules. Chlorine ought to be a common one, but it's hardly ever used.
#2. All pathways are anabolic -- constructive rather than destructive (catabolic) -- that's because the authors were studying autotrophs.
It is striking that the types of organic reactions in core anabolism are limited to 11 chemical transformations: hydrolysis/dehydration, carboxylation/decarboxylation, oxidation/reduction, phosphorylation/dephosphorylation, transamination, group transfer, and isomerization.
This suggests a mechanism for their origin: reusing components developed for other reactions.
#3: No molecule left behind -- no biological molecules go to waste. Autotrophic metabolism uses *everything*.
#4: Five pillars of anabolism -- five methods of fixing carbon that organisms use.
At the present time five different autotrophic pathways have been described (Thauer, 2007; Nakagawa and Takai, 2008) and we chose these for comparison, all having been well established for carbon assimilation: (i) the reductive pentose phosphate pathway (Calvin and Bassham, 1962), (ii) the reductive tricarboxylic acid (rTCA) cycle (Buchanan and Arnon, 1990), (iii) the reductive acetyl-CoA pathway (Ljungdahl, 1986), and (iv) the 3-hydroxypropianate cycle (Ishii et al., 2004) and (v) its variant the 4-hydroxy butyrate cycle (Berg et al., 2007).
Cyanobacteria and chloroplasts and many other bacte use the reductive pentose phosphate cycle, a.k.a. the Calvin-Benson-Bassham cycle.
The reductive tricarboxylic acid cycle is the Krebs cycle run in reverse.
#5: All sugars are phosphorylated -- they all have phosphate groups on them.
#6: All core molecules contain either phosphoric or carboxylic acids or both -- phosphate groups are acidic, and the carboxyl group is -COOH.
The authors speculate as to why this might be.
From the viewpoint of biogenesis, it is possible that this attribute facilitated maximizing the concentration of the core metabolic components by preventing their diffusion through nonpolar, hydrophobic encapsulations or by stabilizing their adsorption on charged surfaces.
#7: The core anabolic network is both brittle and robust -- it does not have much redundancy, but it has lasted for just about all the history of life on our planet.
Then which chemical forms. Nitrogen appears mostly in the most reduced form, as amino groups and the like: -NH2 groups and ==NH groups. Sulfur is likewise most often reduced, as sulfides: -HS groups. Oxygen mainly comes from CO2, H2O, and phosphates.
However, carbon exists in a variety of states. From the most reduced to the most oxidized: CH4, -CH3, -CH2OH, -CHO, -COOH, CO2.
Adding to "monomer" and "polymer" is some words that the authors composed. A "chimeromer" is something assembled from different parts, like Coenzyme A. A "repeatomer" is something assembled from a few repeated parts, like the porphyrin ring.
More on cofactors:
There is a set of about 10 cofactors that seem to be universal across the taxa. An additional 9 cofactors are found in methanogens and acetogens (Ferry and Kastead, 2007).
These include most of the B vitamins and the likes of ATP.
