Functional Map of the Alpha Subunit ofEscherichia coliRNA Polymerase: Amino Acid Substitution within the Amino-terminal Assembly Domain

1995 ◽  
Vol 254 (3) ◽  
pp. 342-349 ◽  
Author(s):  
Makoto Kimura ◽  
Akira Ishihama
1986 ◽  
Vol 261 (23) ◽  
pp. 10475-10477
Author(s):  
R Nishimura ◽  
J Shin ◽  
I Ji ◽  
C R Middaugh ◽  
W Kruggel ◽  
...  

2019 ◽  
Author(s):  
Lu Yang ◽  
Nitin Ravikanthachari ◽  
Ricardo Mariño-Pérez ◽  
Riddhi Deshmukh ◽  
Mariana Wu ◽  
...  

AbstractThe repeated evolutionary specialisation of distantly related insects to cardenolide-containing host plants provides a stunning example of parallel adaptation. Hundreds of herbivorous insect species have independently evolved insensitivity to cardenolides, which are potent inhibitors of the alpha-subunit of Na+, K+-ATPase (ATPα). Previous studies investigating ATPα-mediated cardenolide insensitivity in five insect orders have revealed remarkably high levels of parallelism in the evolution of this trait, including the frequent occurrence of parallel amino acid substitutions at two sites and recurrent episodes of duplication followed by neo-functionalisation. Here we add data for a sixth insect order, Orthoptera, which includes an ancient group of highly aposematic cardenolide-sequestering grasshoppers in the family Pyrgomorphidae. We find that Orthopterans exhibit largely predictable patterns of evolution of insensitivity established by sampling other insect orders. Taken together the data lend further support to the proposal that negative pleiotropic constraints are a key determinant in the evolution of cardenolide insensitivity in insects. Furthermore, analysis of our expanded taxonomic survey implicates positive selection acting on site 111 of cardenolide-sequestering species with a single-copy of ATPα, and sites 115, 118 and 122 in lineages with neo-functionalised duplicate copies, all of which are sites of frequent parallel amino acid substitution.


Biochemistry ◽  
1983 ◽  
Vol 22 (6) ◽  
pp. 1445-1452 ◽  
Author(s):  
C. Robert Matthews ◽  
Mark M. Crisanti ◽  
Joanna T. Manz ◽  
Gary L. Gepner

1993 ◽  
Vol 69 (04) ◽  
pp. 351-360 ◽  
Author(s):  
Masahiro Murakawa ◽  
Takashi Okamura ◽  
Takumi Kamura ◽  
Tsunefumi Shibuya ◽  
Mine Harada ◽  
...  

SummaryThe partial amino acid sequences of fibrinogen Aα-chains from five mammalian species have been inferred by means of the polymerase chain reaction (PCR). From the genomic DNA of the rhesus monkey, pig, dog, mouse and Syrian hamster, the DNA fragments coding for α-C domains in the Aα-chains were amplified and sequenced. In all species examined, four cysteine residues were always conserved at the homologous positions. The carboxy- and amino-terminal portions of the α-C domains showed a considerable homology among the species. However, the sizes of the middle portions, which corresponded to the internal repeat structures, showed an apparent variability because of several insertions and/or deletions. In the rhesus monkey, pig, mouse and Syrian hamster, 13 amino acid tandem repeats fundamentally similar to those in humans and the rat were identified. In the dog, however, tandem repeats were found to consist of 18 amino acids, suggesting an independent multiplication of the canine repeats. The sites of the α-chain cross-linking acceptor and α2-plasmin inhibitor cross-linking donor were not always evolutionally conserved. The arginyl-glycyl-aspartic acid (RGD) sequence was not found in the amplified region of either the rhesus monkey or the pig. In the canine α-C domain, two RGD sequences were identified at the homologous positions to both rat and human RGD S. In the Syrian hamster, a single RGD sequence was found at the same position to that of the rat. Triplication of the RGD sequences was seen in the murine fibrinogen α-C domain around the homologous site to the rat RGDS sequence. These findings are of some interest from the point of view of structure-function and evolutionary relationships in the mammalian fibrinogen Aα-chains.


Author(s):  
Renganayaki G. ◽  
Achuthsankar S. Nair

Sequence alignment algorithms and  database search methods use BLOSUM and PAM substitution matrices constructed from general proteins. These de facto matrices are not optimal to align sequences accurately, for the proteins with markedly different compositional bias in the amino acid.   In this work, a new amino acid substitution matrix is calculated for the disorder and low complexity rich region of Hub proteins, based on residue characteristics. Insights into the amino acid background frequencies and the substitution scores obtained from the Hubsm unveils the  residue substitution patterns which differs from commonly used scoring matrices .When comparing the Hub protein sequences for detecting homologs,  the use of this Hubsm matrix yields better results than PAM and BLOSUM matrices. Usage of Hubsm matrix can be optimal in database search and for the construction of more accurate sequence alignments of Hub proteins.


1996 ◽  
Vol 5 (3) ◽  
pp. 542-545 ◽  
Author(s):  
Kunihiko Gekko ◽  
Youjiro Tamura ◽  
Eiji Ohmae ◽  
Hideyuki Hayashi ◽  
Hiroyuki Kagamiyama ◽  
...  

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