scholarly journals Sugar transport for enhanced xylose utilization in Ashbya gossypii

2020 ◽  
Vol 47 (12) ◽  
pp. 1173-1179
Author(s):  
David Díaz-Fernández ◽  
Gloria Muñoz-Fernández ◽  
Victoria Isabel Martín ◽  
José Luis Revuelta ◽  
Alberto Jiménez
Keyword(s):  
Amino Acid ◽  
Gene Targeting ◽  
Expression Profile ◽  
Industrial Production ◽  
Sugar Transport ◽  
Amino Acid Replacement ◽  
Xylose Utilization ◽  
Ashbya Gossypii ◽  
Hexose Sugars ◽  
Hexose Transporters

AbstractThe co-utilization of mixed (pentose/hexose) sugars constitutes a challenge for microbial fermentations. The fungus Ashbya gossypii, which is currently exploited for the industrial production of riboflavin, has been presented as an efficient biocatalyst for the production of biolipids using xylose-rich substrates. However, the utilization of xylose in A. gossypii is hindered by hexose sugars. Three A. gossypii homologs (AFL204C, AFL205C and AFL207C) of the yeast HXT genes that code for hexose transporters have been identified and characterized by gene-targeting approaches. Significant differences in the expression profile of the HXT homologs were found in response to different concentrations of sugars. More importantly, an amino acid replacement (N355V) in AFL205Cp, introduced by CRISPR/Cas9-mediated genomic edition, notably enhanced the utilization of xylose in the presence of glucose. Hence, the introduction of the afl205c-N355V allele in engineered strains of A. gossypii will further benefit the utilization of mixed sugars in this fungus.

A Novel Polymorphism in Exon 10 of the Factor V Gene Inducing an Amino Acid Replacement of Arginine to Lysine at Codon 485

1997 ◽  
Vol 78 (05) ◽  
pp. 1419-1420 ◽  
Author(s):  
Tetsuo Ozawa ◽  
Kenji Niiya ◽  
Naoko Ejiri ◽  
Nobuo Sakuragawa
Keyword(s):  
Amino Acid ◽  
Amino Acid Replacement ◽  
Factor V ◽  
Factor V Gene ◽  
V Gene ◽  
Exon 10

Assessing the Impact of Secondary Structure and Solvent Accessibility on Protein Evolution

Genetics ◽  
1998 ◽  
Vol 149 (1) ◽  
pp. 445-458 ◽  
Author(s):  
Nick Goldman ◽  
Jeffrey L Thorne ◽  
David T Jones
Keyword(s):  
Amino Acid ◽  
Secondary Structure ◽  
Protein Evolution ◽  
Solvent Accessibility ◽  
Strong Association ◽  
Length Distribution ◽  
Parametric Bootstrap ◽  
Amino Acid Replacement ◽  
Physical Constraints ◽  
The Impact

Abstract Empirically derived models of amino acid replacement are employed to study the association between various physical features of proteins and evolution. The strengths of these associations are statistically evaluated by applying the models of protein evolution to 11 diverse sets of protein sequences. Parametric bootstrap tests indicate that the solvent accessibility status of a site has a particularly strong association with the process of amino acid replacement that it experiences. Significant association between secondary structure environment and the amino acid replacement process is also observed. Careful description of the length distribution of secondary structure elements and of the organization of secondary structure and solvent accessibility along a protein did not always significantly improve the fit of the evolutionary models to the data sets that were analyzed. As indicated by the strength of the association of both solvent accessibility and secondary structure with amino acid replacement, the process of protein evolution—both above and below the species level—will not be well understood until the physical constraints that affect protein evolution are identified and characterized.

scholarly journals Evidence for Selection at the fused1 Locus of Drosophila americana

Genetics ◽  
2001 ◽  
Vol 158 (1) ◽  
pp. 279-290 ◽  
Author(s):  
Jorge Vieira ◽  
Bryant F McAllister ◽  
Brian Charlesworth
Keyword(s):  
Amino Acid ◽  
Sequence Variation ◽  
Amino Acid Replacement ◽  
Population Subdivision ◽  
Amino Acid Substitutions ◽  
Clinal Variation ◽  
Haplotype Structure ◽  
Common Amino Acid ◽  
Chromosome Arrangement ◽  
Dna Sequence Variation

Abstract We analyze genetic variation at fused1, a locus that is close to the centromere of the X chromosome-autosome (X/4) fusion in Drosophila americana. In contrast to other X-linked and autosomal genes, for which a lack of population subdivision in D. americana has been observed at the DNA level, we find strong haplotype structure associated with the alternative chromosomal arrangements. There are several derived fixed differences at fused1 (including one amino acid replacement) between two haplotype classes of this locus. From these results, we obtain an estimate of an age of ∼0.61 million years for the origin of the two haplotypes of the fused1 gene. Haplotypes associated with the X/4 fusion have less DNA sequence variation at fused1 than haplotypes associated with the ancestral chromosome arrangement. The X/4 haplotypes also exhibit clinal variation for the allele frequencies of the three most common amino acid replacement polymorphisms, but not for adjacent silent polymorphisms. These patterns of variation are best explained as a result of selection acting on amino acid substitutions, with geographic variation in selection pressures.

scholarly journals An alternative model of amino acid replacement

2004 ◽  
Vol 21 (7) ◽  
pp. 975-980 ◽  
Author(s):  
G. E. Crooks ◽  
S. E. Brenner
Keyword(s):  
Amino Acid ◽  
Alternative Model ◽  
Amino Acid Replacement

scholarly journals Nucleotide Variation and Conservation at the dpp Locus, a Gene Controlling Early Development in Drosophila

Genetics ◽  
1997 ◽  
Vol 145 (2) ◽  
pp. 311-323 ◽  
Author(s):  
Brent Richter ◽  
Manyuan Long ◽  
R C Lewontin ◽  
Eiji Nitasaka
Keyword(s):  
Linkage Disequilibrium ◽  
Amino Acid ◽  
Gene Conversion ◽  
Haplotype Diversity ◽  
Amino Acid Replacement ◽  
Nucleotide Variation ◽  
Nucleotide Level ◽  
Untranslated Sequence ◽  
Gene Coding ◽  
Large Intron

A study of polymorphism and species divergence of the dpp gene of Drosophila has been made. Eighteen lines from a population of D. melanogaster were sequenced for 5200 bp of the Hin region of the gene, coding for the dpp polypeptide. A comparison was made with sequence from D. simulans. Ninety-six silent polymorphisms and three amino acid replacement polymorphisms were found. The overall silent polymorphism (0.0247) is low, but haplotype diversity (0.0066 for effectively silent sites and 0.0054 for all sites) is in the range found for enzyme loci. Amino acid variation is absent in the N-terminal signal peptide, the C-terminal TGF-β peptide and in the N-terminal half of the pro-protein region. At the nucleotide level there is strong conservation in the middle half of the large intron and in the 3′ untranslated sequence of the last exon. The 3′ untranslated conservation, which is perfect for 110 bp among all the divergent species, is unexplained. There is strong positive linkage disequilibrium among polymorphic sites, with stretches of apparent gene conversion among originally divergent sequences. The population apparently is a migration mixture of divergent clades.

Evolutionary divergence and salinity-mediated selection in halophilic archaea

1997 ◽  
Vol 61 (1) ◽  
pp. 90-104
Author(s):  
P P Dennis ◽  
L C Shimmin
Keyword(s):  
Amino Acid ◽  
Tertiary Structure ◽  
Halophilic Archaea ◽  
Amino Acid Replacement ◽  
Evolutionary Divergence ◽  
Ionic Balance ◽  
Amino Acid Residues ◽  
Nucleotide Substitutions ◽  
Nonsynonymous Substitutions ◽  
Environmental Salinity

Halophilic (literally salt-loving) archaea are a highly evolved group of organisms that are uniquely able to survive in and exploit hypersaline environments. In this review, we examine the potential interplay between fluctuations in environmental salinity and the primary sequence and tertiary structure of halophilic proteins. The proteins of halophilic archaea are highly adapted and magnificently engineered to function in an intracellular milieu that is in ionic balance with an external environment containing between 2 and 5 M inorganic salt. To understand the nature of halophilic adaptation and to visualize this interplay, the sequences of genes encoding the L11, L1, L10, and L12 proteins of the large ribosome subunit and Mn/Fe superoxide dismutase proteins from three genera of halophilic archaea have been aligned and analyzed for the presence of synonymous and nonsynonymous nucleotide substitutions. Compared to homologous eubacterial genes, these halophilic genes exhibit an inordinately high proportion of nonsynonymous nucleotide substitutions that result in amino acid replacement in the encoded proteins. More than one-third of the replacements involve acidic amino acid residues. We suggest that fluctuations in environmental salinity provide the driving force for fixation of the excessive number of nonsynonymous substitutions. Tinkering with the number, location, and arrangement of acidic and other amino acid residues influences the fitness (i.e., hydrophobicity, surface hydration, and structural stability) of the halophilic protein. Tinkering is also evident at halophilic protein positions monomorphic or polymorphic for serine; more than one-third of these positions use both the TCN and the AGY serine codons, indicating that there have been multiple nonsynonymous substitutions at these positions. Our model suggests that fluctuating environmental salinity prevents optimization of fitness for many halophilic proteins and helps to explain the unusual evolutionary divergence of their encoding genes.

Location of amphipathic α-helical domain in CRF using HPLC retention data of double D-amino acid replacement set

Peptides 1994 ◽  
1995 ◽  
pp. 420-421
Author(s):  
E. Krause ◽  
M. Beyermann ◽  
M. Dathe ◽  
S. Rothemund ◽  
G. Krause ◽  
...  
Keyword(s):  
Amino Acid ◽  
Amino Acid Replacement ◽  
Retention Data ◽  
Helical Domain

Amino acid and hexose transport by cultured crypt cells from rat small intestine

1980 ◽  
Vol 239 (5) ◽  
pp. C190-C196 ◽  
Author(s):  
K. Inui ◽  
A. Quaroni ◽  
L. G. Tillotson ◽  
K. J. Isselbacher
Keyword(s):  
Amino Acid ◽  
Sugar Transport ◽  
Epithelial Cell Line ◽  
Acid Uptake ◽  
Substrate Uptake ◽  
Hexose Transport ◽  
Intestinal Crypt ◽  
Morphological Criteria ◽  
Hexose Uptake ◽  
Crypt Cells

The characteristics of amino acid and sugar transport in intestinal crypt epithelial cells have been examined by measuring substrate uptake in an established epithelial cell line. These cells (IEC-6 cells) have been characterized as derived from rat small intestinal crypt cells on the basis of morphological criteria (J. Cell. Biol. 80: 248-265, 1979). Amino acid transport appeared to be mediated by both Na+-dependent and Na+-independent systems. Hexose uptake was stereospecific and Na+ independent, and was markedly inhibited by phloretin and cytochalasin B. Since glucocorticoids are known to have profound effects on maturation of the intestinal epithelium in vivo, their effects on transport properties of the cultured crypt cells were studied. Hydrocortisone, while completely inhibiting cell growth, increased the initial uptake rates of various hexoses, while having little or nor effect on the initial rate of amino acid uptake. The increased hexose uptake appeared to be due to a change in Vmax rather than Km. Appearance of the Na+-dependent hexose transport system, which is present in differentiated enterocytes, was not elicited by in vitro treatment with glucocortcoids.

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