Horizontal gene transfer from Eukarya to Bacteria and domain shuffling: the ?-amylase model

Abstract

Alpha-amylases are present in all kingdoms of the living world. Despite strong conservation of the tertiary structure, only a few amino acids are conserved in interkingdom comparisons. Animal alpha-amylases are characterized by several typical motifs and biochemical properties. A few cases of such alpha-amylases have been previously reported in some eubacterial species. We screened the bacterial genomes available in the sequence databases for new occurrences of animal-like alpha-amylases. Three novel cases were found, which belong to unrelated bacterial phyla: Chloroflexus aurantiacus, Microbulbifer degradans, and Thermobifida fusca. All the animal-like alpha-amylases in Bacteria probably result from repeated horizontal gene transfer from animals. The M. degradans genome also contains bacterial-type and plant-type alpha-amylases in addition to the animal-type one. Thus, this species exhibits alpha-amylases of animal, plant, and bacterial origins. Moreover, the similarities in the extra C-terminal domains (different from both the alpha-amylase domain C and the starch-binding domain), when present, also suggest interkingdom as well as intragenomic shuffling.

Phylogenetic and biochemical characterization of a novel cluster of intracellular fungal α-amylase enzymes

“…The recently identified a-glucanotransferases AgtA and AgtB cluster with the extracellular fungal aamylases, rather than with the intracellular group. The bacterial a-amylases form several clusters in the tree, reflecting their sequence similarities to enzymes from fungi, plants or animals, as described previously (Janecek, 1994;Janecek et al, 1999;Da Lage et al, 2004).The 13 putative intracellular fungal a-amylases share several sequence features with the bacterial enzymes in the GH13_5 family. These features are, or may be, invariant among the intracellular fungal enzymes and the related bacterial enzymes, but in most cases have no (conserved) equivalent in the other a-amylases studied here (Fig.…”

“…The recently identified a-glucanotransferases AgtA and AgtB cluster with the extracellular fungal aamylases, rather than with the intracellular group. The bacterial a-amylases form several clusters in the tree, reflecting their sequence similarities to enzymes from fungi, plants or animals, as described previously (Janecek, 1994;Janecek et al, 1999;Da Lage et al, 2004).…”

“…The set was supplemented with the 12 fungal sequences identified as described above, and three additional sequences: Amy1p from H. capsulatum (Marion et al, 2006), and AgtA (An09g03100) and AgtB (An12g02460) from A. niger. The alignment strategy was based on the approach described by Da Lage et al (2004). In brief, (i) the best conserved regions, the b1, b2, b3, b4, b5, b7 and b8 strands of the catalytic (b/a) 8 barrel and region V of domain B (Janecek, 2002), were identified in each sequence; (ii) the segments preceding and succeeding the regions around strands b1 and b8, respectively, were cut off; (iii) the shortened sequences (amino acids 34-435 in AmyD) were aligned with the CLUSTAL W program (Thompson et al, 1994); (iv) the identified conserved sequence regions were aligned manually, if necessary; and (v) the remaining parts of the alignment (between the regions) were manually tuned where applicable.…”

Enzymatic properties and primary structures of two α-amylase isozymes from the Pacific abalone Haliotis discus hannai

“…Accordingly, the C-terminal approximately 190 residues of HdAmy82 was revealed to be the specific region that was absent in HdAmy58. This region was considered as an ancillary domain of HdAmy82 since it showed considerably high sequence similarities to the ancillary domains of several -amylases previously reported (Da Lage et al, 2004).…”

“…7A and B). Some of GHF-13 -amylases are known to possess the family-20-type carbohydrate-binding modules (CBM) (Da-Lage et al 2004). …”