Bioinformatics

Among the more than 400 families of transport systems in our TC system, very few include integral membrane homologues that function in a capacity other than transport. Moreover, almost all these exceptions are receptors. In some cases, transporters gained receptor functions while retaining their transport functions but in other cases they gained this function while losing the capacity to transport. A loss of transport capacity typically is accompanied by the gain or loss of specific protein domains, in a few cases, another protein with high affinity for the transport protein homologue accounts for the loss of function. Dissociation of such protein-protein complexes or losing the extra domains may restore the lost transport functions.

After analyzing dozens of large transport protein families, we find several examples of horizontal transfer between distinct kingdoms within these domains, such as between gram-positive and gram-negative bacteria. However, we find little evidence of horizontal transfer of transporter genes among the three domains occurring any time during the past two billion years. Thus, although hundreds of members of the MC family are found in eukaryotes, not a single such member is found in a prokaryote. Moreover, of the hundreds of sequenced homologues of the phosphoenolpyruvate, sugar phosphotransferase system (PTS), every one is in a bacterium, without a single example in an archaeon or a eukaryote.

After analyzing numerous multicomponent transport systems phylogenetically, we found little evidence for shuffling of protein constituents during their late evolutionary divergence. We included several protein secretion systems, such as types I, II, III, and IV as well as ABC-type solute uptake systems. The protein secretion systems consist of many proteins that were often transferred laterally among gram-negative bacteria. Although several such multicomponent systems may be found within a single bacterial cell, the systems apparently did not exchange protein constituents, even though they can be exchanged experimentally by genetic manipulation. One important caveat: phylogenetic analyses may overlook constituent shuffling between closely related systems.

These observations suggest to us that complex multicomponent transport systems depend on extensive protein-protein interactions, which probably arose through coevolution of the protein constituents. Once any two systems have diverged appreciably in sequence, the constituents in one system no longer can interact properly with those in another, effectively preventing shuffling between the two.

Step 1. Assemble your sequences.

Put all your sequences in Fasta format in a single file.

This file should be located in a suitably named

subdirectory of your home directory on the UBiC Blast

server. The definition line for each sequence should start

with a unique identifier for that sequence.

Step 2. Convert this sequence file to a Blastable database.

The command formatdb converts your Fasta file of sequences

to a set of files that can be queried with command-line

BLAST.

Step 3. Test Blast on your database.

See the UBiC tutorial, Using Command-line BLAST. In the

blastall command-line you will need to specify the location

of your database by typing: -

d /disk2/home/myhome/blastdbs/custom.aa.

Many integral membrane transport proteins contain 6 or 12 TMSs. For example, both mitochondrial carrier (MC) family members and the aquaporins and glycerol facilitators within the major intrinsic protein (MIP) family contain six TMSs per polypeptide chain. Sequence analyses reveal that MIP family members arose by duplication of a three-TMS-encoding genetic element, while members of the MC family arose by triplication of a two-TMS-encoding element.

The MIP family arose before the three domains of life (bacteria, archaea, and eukaryotes) diverged from each other, whereas the MC family arose late within eukaryotes, after endosymbiotic proteobacteria became permanent denizens of eukaryotic cells. The advent of mitochondria evidently required a new mode of communication between the mitochondrial matrix and the cytoplasmic compartment of such cells. Thus, mitochondrial carriers depend on a distinctive solute. Solute exchange mechanism rather than on the cation symport mechanisms that bacteria use for ingesting nutrients.

My background is in computer sciences, including design of algorithms and theoretical computer science. I got interested in this because of some work in an area called DNA computing. That idea is to build computers out of DNA. The person who started that line of work - is a computer scientist who spent a quite a bit of time in a biology lab. His work really caught the attention of many people in the computer science community. But then, as I got more interested in some of the algorithmic problems that come up, I realized they are also relevant in the more traditional biological areas. You have to talk to chemists and biochemists if you want to understand DNA and RNA - you can’t get the right level of understanding just from reading papers. I got more interested in their perspectives and problems.

MDR efflux pumps began causing clinical problems relatively recently, in parallel with the extensive use of antibiotics in medicine and as supplements in animal feeds. However, our analyses indicate that these MDR efflux pumps did not arise through recent mutations in genes encoding transporters that changed their substrate specificities.

Instead, such MDR pumps are encoded within the genomes of virtually all microorganisms, so these genes are present and thus need only to be activated to become problematic. Moreover, lateral transfer of genes among bacteria has occurred frequently, particularly for plasmid-encoded systems, suggesting that such genes can be acquired fairly readily even if they are not initially present. Finally, although mutations that enable transporters to act on different types of substrate are rare, experiments and phylogenetic analyses indicate that simple point mutations can readily narrow or broaden a particular transporter's specificity toward a single class of compounds. These findings provide clues for developing strategies to control MDR among bacterial pathogens.