Close Evolutionary Relatedness of α-Amylases from Archaea and Plants

Abstract

Abstract. The amino acid sequences of 22 ␣-amylases from family 13 of glycosyl hydrolases were analyzed with the aim of revealing the evolutionary relationships between the archaeal ␣-amylases and their eubacterial and eukaryotic counterparts. Two evolutionary distance trees were constructed: (i) the first one based on the alignment of extracted best-conserved sequence regions (58 residues) comprising ␤2, ␤3, ␤4, ␤5, ␤7, and ␤8 strand segments of the catalytic (␣/␤) 8 -barrel and a short conserved stretch in domain B protruding out of the barrel in the ␤3 → ␣3 loop, and (ii) the second one based on the alignment of the substantial continuous part of the (␣/␤) 8 -barrel involving the entire domain B (consensus length: 386 residues). With regard to archaeal ␣-amylases, both trees compared brought, in fact, the same results; i.e., all family 13 ␣-amylases from domain Archaea were clustered with barley pI isozymes, which represent all plant ␣-amylases. The enzymes from Bacillus licheniformis and Escherichia coli, representing liquefying and cytoplasmic ␣-amylases, respectively, seem to be the further closest relatives to archaeal ␣-amylases. This evolutionary relatedness clearly reflects the discussed similarities in the amino acid sequences of these ␣-amylases, especially in the bestconserved sequence regions. Since the results for ␣-amylases belonging to all three domains (Eucarya, Eubacteria, Archaea) offered by both evolutionary trees are very similar, it is proposed that the investigated conserved sequence regions may indeed constitute the ''sequence fingerprints'' of a given ␣-amylase.

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).…”

New insight in cereal starch degradation: identification and structural characterization of four α-amylases in bread wheat

“…Available amino acid sequences were taken from a few previous bioinformatics studies [5,[26][27][28][29][30] focusing mainly on the α-amylases from subfamilies GH13_6 (29 plant α-amylases accompanied by 2 bacterial representatives) and GH13_7 (10 archaeal and 2 bacterial sources). These 43 sequences, retrieved from the UniProt knowledge database ( [31]; http://www.uniprot.org/), were completed by the consensus protein sequence for each wheat isoform.…”

“…A difference in distance between amino acid residues between the isoforms is highlighted in yellow in the TaAMY3. but indicative differences within their conserved sequence regions [4,26,29].…”

“…Based on the observed relationships, the members of isoforms TaAMY1 and TaAMY2 may very probably represent high and low pI α-amylase isozymes, respectively, since they are grouped with well-characterized α-amylase isozymes from barley, i.e. TaAMY1 with high pI isozyme representatives previously classified in the original plant subfamily GH13_6 were added together with their prokaryotic counterparts from the most closely related subfamily GH13_7 [26], covering only the α-amylases from archaeons and bacteria [29]. In agreement with the CAZy classification [51], the two GH13 subfamilies are clearly separated from each other.…”