Transcript microbes world

MICROBES SPANNING THE WORLD:
Exploring Phylogenetic Relationships and Protein Structure
Isocitrate lyase can cleave isocitrate producing glyoxylate and succinate.
Researchers have identified two amino acid changes in the active site that allow
the enzyme to function at lower temperatures. The cold-adapted icl gene sequence
is longer than sequence found in most mesophiles.
How does the isocitrate lyase from your favorite organism compare to other
microorganisms?
Are isolates from the Siberian permafrost closely related to other bacteria
isolated from around the world?
This research project will allow students to identify bacteria from their favorite
local environment and compare the 16S rRNA gene sequence of their isolate to
those of bacteria isolated all over the world. Students can choose and compare the
effect of the environment on protein structure. Here we choose to look at the
effect of temperature on bacterial diversity and on isocitrate lyase structure.
Space filling diagram of the 3D structure of isocitrate lyase. The PDB file for
Mycobacterium tuberculosis isocitrate lyase (1f61) was used as a reference
and sequence information from our representative psychrotolerant, mesophilic
and thermophilic target organisms was used in Consurf to construct the
structure. The black residues are highly conserved amongst all the sequences.
The red colored residue is a lysine (K) in thermophilic and mesophilic
organisms and a glutamine (Q) in the psychrotolerant organisms.
How widely distributed is the genus? What environment niches does your
organism occupy? Does environment impact the structure of key proteins and
enzymes?
For this example:
Hypothesis: We propose that Psychrobacter arcticus, which was isolated from the
Siberian permafrost, is closely related to other cold-adapted microorganisms and
that the structure of isocitrate lyase will have cold-adapted modifications.
16S rRNA Sequences Isolated at Princeton
Alignment of aminoacid sequences and Clustal W Tree of Isocitrate Lyase
from several psychrotolerant, mesophilic, and thermophilic organisms.
Alignments were done in Workbench.