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1.  The Role of Energy in the Emergence of Biology from Chemistry 
Any scenario of the transition from chemistry to biology should include an “energy module” because life can exist only when supported by energy flow(s). We addressed the problem of primordial energetics by combining physico-chemical considerations with phylogenomic analysis. We propose that the first replicators could use abiotically formed, exceptionally photostable activated nucleotides both as building blocks and as the main energy source. Nucleoside triphosphates could replace cyclic nucleotides as the principal energy-rich compounds at the stage of the first cells, presumably because the metal chelates of nucleoside triphosphates penetrated membranes much better than the respective metal complexes of nucleoside monophosphates. The ability to exploit natural energy flows for biogenic production of energy-rich molecules could evolve only gradually, after the emergence of sophisticated enzymes and ion-tight membranes. We argue that, in the course of evolution, sodium-dependent membrane energetics preceded the proton-based energetics which evolved independently in bacteria and archaea.
doi:10.1007/s11084-012-9308-z
PMCID: PMC3974900  PMID: 23100130
2.  Planctomycetes and eukaryotes: a case of analogy not homology 
Summary
Planctomycetes, Verrucomicrobia and Chlamydia are prokaryotic phyla that are sometimes grouped together as the PVC superphylum of eubacteria. Some PVC species possess interesting attributes, in particular, internal membranes that superficially resemble eukaryotic endomembranes. Some biologists now claim that PVC bacteria are nucleus-bearing prokaryotes and that they are evolutionary intermediates in the transition from prokaryote to eukaryote. PVC prokaryotes do not possess a nucleus and are not intermediates in the prokaryote-to-eukaryote transition. All of the PVC traits that are currently cited as evidence for aspiring eukaryoticity are either analogous (the result of convergent evolution), not homologous, to eukaryotic traits; or else they are the result of lateral gene transfers. Here we summarize the evidence that shows why most of the purported similarities between the PVC bacteria and eukaryotes are analogous and the rest are consequence of lateral gene acquisition.
doi:10.1002/bies.201100045
PMCID: PMC3795523  PMID: 21858844
3.  Divergence and Convergence in Enzyme Evolution* 
Comparative analysis of the sequences of enzymes encoded in a variety of prokaryotic and eukaryotic genomes reveals convergence and divergence at several levels. Functional convergence can be inferred when structurally distinct and hence non-homologous enzymes show the ability to catalyze the same biochemical reaction. In contrast, as a result of functional diversification, many structurally similar enzyme molecules act on substantially distinct substrates and catalyze diverse biochemical reactions. Here, we present updates on the ATP-grasp, alkaline phosphatase, cupin, HD hydrolase, and N-terminal nucleophile (Ntn) hydrolase enzyme superfamilies and discuss the patterns of sequence and structural conservation and diversity within these superfamilies. Typically, enzymes within a superfamily possess common sequence motifs and key active site residues, as well as (predicted) reaction mechanisms. These observations suggest that the strained conformation (the entatic state) of the active site, which is responsible for the substrate binding and formation of the transition complex, tends to be conserved within enzyme superfamilies. The subsequent fate of the transition complex is not necessarily conserved and depends on the details of the structures of the enzyme and the substrate. This variability of reaction outcomes limits the ability of sequence analysis to predict the exact enzymatic activities of newly sequenced gene products. Nevertheless, sequence-based (super)family assignments and generic functional predictions, even if imprecise, provide valuable leads for experimental studies and remain the best approach to the functional annotation of uncharacterized proteins from new genomes.
doi:10.1074/jbc.R111.241976
PMCID: PMC3249071  PMID: 22069324
Enzyme Catalysis; Enzyme Mechanisms; Enzyme Structure; Evolution; Phosphodiesterases; Convergence; Divergence
4.  From complete genome sequence to “complete“ understanding? 
Trends in biotechnology  2010;28(8):398-406.
The rapidly accumulating genome sequence data allow researchers to address fundamental biological questions that were not even asked just a few years ago. A major problem in genomics is the widening gap between the rapid progress in genome sequencing and the comparatively slow progress in the functional characterization of sequenced genomes. Here we discuss two key questions of genome biology: whether we need more genomes, and how deep is our understanding of biology based on genomic analysis. We argue that overly specific annotations of gene functions are often less useful than the more generic, but also more robust, functional assignments based on protein family classification. We also discuss problems in understanding the functions of the remaining “conserved hypothetical” genes.
doi:10.1016/j.tibtech.2010.05.006
PMCID: PMC3065831  PMID: 20647113
5.  Co-evolution of primordial membranes and membrane proteins 
Trends in biochemical sciences  2009;34(4):206-215.
Studies of the past several decades have provided major insights into the structural organization of biological membranes and mechanisms of many membrane molecular machines. However, the origin(s) of the membrane(s) and membrane proteins remain enigmatic. We discuss different concepts of the origin and early evolution of membranes, with a focus on the evolution of the (im)permeability to charged molecules, such as proteins and nucleic acids, and small ions. Reconstruction of the evolution of F-type and A/V-type membrane ATPases (ATP synthases), which are either proton or sodium-dependent, might help understand not only the origin of membrane bioenergetics, but also of membranes themselves. We argue that evolution of biological membranes occurred as a process of co-evolution of lipid bilayers, membrane proteins and membrane bioenergetics.
doi:10.1016/j.tibs.2009.01.005
PMCID: PMC2752816  PMID: 19303305
6.  ‘Conserved hypothetical’ proteins: prioritization of targets for experimental study 
Nucleic Acids Research  2004;32(18):5452-5463.
Comparative genomics shows that a substantial fraction of the genes in sequenced genomes encodes ‘conserved hypothetical’ proteins, i.e. those that are found in organisms from several phylogenetic lineages but have not been functionally characterized. Here, we briefly discuss recent progress in functional characterization of prokaryotic ‘conserved hypothetical’ proteins and the possible criteria for prioritizing targets for experimental study. Based on these criteria, the chief one being wide phyletic spread, we offer two ‘top 10’ lists of highly attractive targets. The first list consists of proteins for which biochemical activity could be predicted with reasonable confidence but the biological function was predicted only in general terms, if at all (‘known unknowns’). The second list includes proteins for which there is no prediction of biochemical activity, even if, for some, general biological clues exist (‘unknown unknowns’). The experimental characterization of these and other ‘conserved hypothetical’ proteins is expected to reveal new, crucial aspects of microbial biology and could also lead to better functional prediction for medically relevant human homologs.
doi:10.1093/nar/gkh885
PMCID: PMC524295  PMID: 15479782
7.  The COG database: a tool for genome-scale analysis of protein functions and evolution 
Nucleic Acids Research  2000;28(1):33-36.
Rational classification of proteins encoded in sequenced genomes is critical for making the genome sequences maximally useful for functional and evolutionary studies. The database of Clusters of Orthologous Groups of proteins (COGs) is an attempt on a phylogenetic classification of the proteins encoded in 21 complete genomes of bacteria, archaea and eukaryotes (http://www.ncbi.nlm.nih.gov/COG ). The COGs were constructed by applying the criterion of consistency of genome-specific best hits to the results of an exhaustive comparison of all protein sequences from these genomes. The database comprises 2091 COGs that include 56–83% of the gene products from each of the complete bacterial and archaeal genomes and ~35% of those from the yeast Saccharomyces cerevisiae genome. The COG database is accompanied by the COGNITOR program that is used to fit new proteins into the COGs and can be applied to functional and phylogenetic annotation of newly sequenced genomes.
PMCID: PMC102395  PMID: 10592175

Results 1-7 (7)