scholarly journals Lateral Gene Transfer Acts As an Evolutionary Shortcut to Efficient C4 Biochemistry

2020 ◽  
Vol 37 (11) ◽  
pp. 3094-3104
Author(s):  
Chatchawal Phansopa ◽  
Luke T Dunning ◽  
James D Reid ◽  
Pascal-Antoine Christin
Keyword(s):  
Genetic Variation ◽  
Amino Acid ◽  
Gene Transfer ◽  
Catalytic Efficiency ◽  
Distinct Species ◽  
Amino Acid Replacement ◽  
The Novel ◽  
Ideal System ◽  
Genes Encoding ◽  
Speed Up

Abstract The adaptation of proteins for novel functions often requires changes in their kinetics via amino acid replacement. This process can require multiple mutations, and therefore extended periods of selection. The transfer of genes among distinct species might speed up the process, by providing proteins already adapted for the novel function. However, this hypothesis remains untested in multicellular eukaryotes. The grass Alloteropsis is an ideal system to test this hypothesis due to its diversity of genes encoding phosphoenolpyruvate carboxylase, an enzyme that catalyzes one of the key reactions in the C4 pathway. Different accessions of Alloteropsis either use native isoforms relatively recently co-opted from other functions or isoforms that were laterally acquired from distantly related species that evolved the C4 trait much earlier. By comparing the enzyme kinetics, we show that native isoforms with few amino acid replacements have substrate KM values similar to the non-C4 ancestral form, but exhibit marked increases in catalytic efficiency. The co-option of native isoforms was therefore followed by rapid catalytic improvements, which appear to rely on standing genetic variation observed within one species. Native C4 isoforms with more amino acid replacements exhibit additional changes in affinities, suggesting that the initial catalytic improvements are followed by gradual modifications. Finally, laterally acquired genes show both strong increases in catalytic efficiency and important changes in substrate handling. We conclude that the transfer of genes among distant species sharing the same physiological novelty creates an evolutionary shortcut toward more efficient enzymes, effectively accelerating evolution.

scholarly journals Localized Hypermutation is the Major Driver of Meningococcal Genetic Variability during Persistent Asymptomatic Carriage

mBio ◽  
2020 ◽  
Vol 11 (2) ◽  
Author(s):  
Luke R. Green ◽  
Ali A. Al-Rubaiawi ◽  
Mohammad A. R. M. Al-Maeni ◽  
Odile B. Harrison ◽  
Matthew Blades ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Gene Transfer ◽  
Outer Membrane ◽  
Antigenic Variation ◽  
Allelic Variation ◽  
Host Responses ◽  
Content Type ◽  
Type Iv ◽  
Asymptomatic Carriage ◽  
Genes Encoding

ABSTRACT Host persistence of bacteria is facilitated by mutational and recombinatorial processes that counteract loss of genetic variation during transmission and selection from evolving host responses. Genetic variation was investigated during persistent asymptomatic carriage of Neisseria meningitidis. Interrogation of whole-genome sequences for paired isolates from 25 carriers showed that de novo mutations were infrequent, while horizontal gene transfer occurred in 16% of carriers. Examination of multiple isolates per time point enabled separation of sporadic and transient allelic variation from directional variation. A comprehensive comparative analysis of directional allelic variation with hypermutation of simple sequence repeats and hyperrecombination of class 1 type IV pilus genes detected an average of seven events per carrier and 2:1 bias for changes due to localized hypermutation. Directional genetic variation was focused on the outer membrane with 69% of events occurring in genes encoding enzymatic modifiers of surface structures or outer membrane proteins. Multiple carriers exhibited directional and opposed switching of allelic variants of the surface-located Opa proteins that enables continuous expression of these adhesins alongside antigenic variation. A trend for switching from PilC1 to PilC2 expression was detected, indicating selection for specific alterations in the activities of the type IV pilus, whereas phase variation of restriction modification (RM) systems, as well as associated phasevarions, was infrequent. We conclude that asymptomatic meningococcal carriage on mucosal surfaces is facilitated by frequent localized hypermutation and horizontal gene transfer affecting genes encoding surface modifiers such that optimization of adhesive functions occurs alongside escape of immune responses by antigenic variation. IMPORTANCE Many bacterial pathogens coexist with host organisms, rarely causing disease while adapting to host responses. Neisseria meningitidis, a major cause of meningitis and septicemia, is a frequent persistent colonizer of asymptomatic teenagers/young adults. To assess how genetic variation contributes to host persistence, whole-genome sequencing and hypermutable sequence analyses were performed on multiple isolates obtained from students naturally colonized with meningococci. High frequencies of gene transfer were observed, occurring in 16% of carriers and affecting 51% of all nonhypermutable variable genes. Comparative analyses showed that hypermutable sequences were the major mechanism of variation, causing 2-fold more changes in gene function than other mechanisms. Genetic variation was focused on genes affecting the outer membrane, with directional changes in proteins responsible for bacterial adhesion to host surfaces. This comprehensive examination of genetic plasticity in individual hosts provides a significant new platform for rationale design of approaches to prevent the spread of this pathogen.

scholarly journals Inhibitor-resistant TEM (IRT) beta-lactamases with different substitutions at position 244.

1997 ◽  
Vol 41 (11) ◽  
pp. 2547-2549 ◽  
Author(s):  
L Bret ◽  
E B Chaibi ◽  
C Chanal-Claris ◽  
D Sirot ◽  
R Labia ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Amino Acid ◽  
Amino Acid Sequence ◽  
Amino Acid Replacement ◽  
Beta Lactamase ◽  
The Novel ◽  
Beta Lactamases ◽  
Coli Isolate ◽  
Amoxicillin Clavulanate

A novel inhibitor-resistant TEM (IRT) beta-lactamase was detected in an Escherichia coli isolate resistant to amoxicillin-clavulanate and susceptible to cephalothin. The substrate and inhibitor profiles of this beta-lactamase were similar to those of IRT-1 and IRT-2. The novel IRT's bla gene was sequenced, and the deduced amino acid sequence showed the amino acid replacement Arg for His-244 of the TEM-1 sequence. Substitutions for Arg-244 have been reported in three TEM-1 mutants: IRT-1 (which corresponds to TEM-31) (Cys), IRT-2/TEM-30 (Ser), and TEM-41 (Thr). We designated this novel beta-lactamase, which corresponds to TEM-51, IRT-15.

scholarly journals Mutation Spectra and the Neutrality of Mutations

1974 ◽  
Vol 27 (3) ◽  
pp. 309 ◽  
Author(s):  
J Langridge
Keyword(s):  
Amino Acid ◽  
Catalytic Efficiency ◽  
Amino Acid Replacement ◽  
Enzyme Function ◽  
Substrate Affinity ◽  
Amino Acid Substitutions ◽  
Galactosidase Activity ◽  
Immunological Tests ◽  
Normal Enzyme ◽  
Mutation Spectra

The effect of amino acid replacements on enzyme function was studied in the tJ-galactosidase of Escherichia coli. Mutants possessing 50% or less of normal enzyme activity were isolated and examined. Of 733 amino acid substitutions calculated to have occurred, only 11 reduced tJ-galactosidase activity below 50 %. These mutations were expressed because they greatly impaired the substrate affinity or catalytic efficiency of the enzyme. The inertness of the enzyme to amino acid replacement was confirmed by immunological tests of tJ-galactosidase molecules changed in amino acid sequence by suppression.

scholarly journals Use of in vitro mutagenesis to analyze the molecular basis of the difference in Adh expression associated with the allozyme polymorphism in Drosophila melanogaster.

Genetics ◽  
1991 ◽  
Vol 129 (2) ◽  
pp. 481-488
Author(s):  
M Choudhary ◽  
C C Laurie
Keyword(s):  
Drosophila Melanogaster ◽  
Amino Acid ◽  
Protein Level ◽  
Molecular Basis ◽  
Catalytic Efficiency ◽  
Amino Acid Replacement ◽  
Single Amino Acid ◽  
In Vitro Mutagenesis ◽  
The Difference

Abstract In natural populations of Drosophila melanogaster, the alcohol dehydrogenase (Adh) locus is polymorphic for two allozymes, designated Slow and Fast. Fast homozygotes generally have a two- to threefold higher ADH activity level than Slow homozygotes for two reasons: they have a higher concentration of ADH protein and the Fast protein has a higher catalytic efficiency. DNA sequencing studies have shown that the two allozymes generally differ by only a single amino acid at residue 192, which must therefore be the cause of the catalytic efficiency difference. A previous P element-transformation experiment mapped the difference in ADH protein level to a 2.3-kb HpaI/ClaI restriction fragment; which contains all of the Adh coding sequences but excludes all of the 5' flanking region of the distal transcriptional unit. Here we report the results of a site-directed in vitro mutagenesis experiment designed to investigate the effects of the amino acid replacement. This replacement has the expected effect on catalytic efficiency, but there is no detectable effect on the concentration of ADH protein estimated immunologically. This result shows that the average difference in ADH protein level between the allozymic classes is due to linkage disequilibrium between the amino acid replacement and one or more other polymorphisms within the HpaI/ClaI fragment. Sequence analysis of several Fast and Slow alleles suggested that the other polymorphism might be a silent substitution at nucleotide 1443, but another in vitro mutagenesis experiment reported here shows that this is not the case. Therefore, the molecular basis of the difference in ADH protein concentration between the allozymic classes remains an open question.

scholarly journals Novel Cefotaximase (CTX-M-16) with Increased Catalytic Efficiency Due to Substitution Asp-240→Gly

2001 ◽  
Vol 45 (8) ◽  
pp. 2269-2275 ◽  
Author(s):  
R. Bonnet ◽  
C. Dutour ◽  
J. L. M. Sampaio ◽  
C. Chanal ◽  
D. Sirot ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Amino Acid ◽  
Amino Acid Sequence ◽  
Catalytic Efficiency ◽  
Enterobacter Cloacae ◽  
E Coli ◽  
Genes Encoding ◽  
Encoding Gene ◽  
Synergy Test ◽  
Encoding Genes

ABSTRACT Three clinical strains (Escherichia coli Rio-6,E. coli Rio-7, and Enterobacter cloacae Rio-9) collected in 1996 and 1999 from hospitals in Rio de Janeiro (Brazil) were resistant to broad-spectrum cephalosporins and gave a positive double-disk synergy test. Two bla CTX-M genes encoding β-lactamases of pl 7.9 and 8.2 were implicated in this resistance: the bla CTX-M-9 gene observed inE. coli Rio-7 and E. cloacae Rio-9 and a novel CTX-M-encoding gene, designated bla CTX-M-16, observed in E. coli strain Rio-6. The deduced amino acid sequence of CTX-M-16 differed from CTX-M-9 only by the substitution Asp-240→Gly. The CTX-M-16-producing E. coli transformant exhibited the same level of resistance to cefotaxime (MIC, 16 μg/ml) but had a higher MIC of ceftazidime (MIC, 8 versus 1 μg/ml) than the CTX-M-9-producing transformant. Enzymatic studies revealed that CTX-M-16 had a 13-fold higher affinity for aztreonam and a 7.5-fold higher kcat for ceftazidime than CTX-M-9, thereby showing that the residue in position 240 can modulate the enzymatic properties of CTX-M enzymes. The two bla CTX-M-9 genes and the bla CTX-M-16 gene were located on different plasmids, suggesting the presence of mobile elements associated with CTX-M-encoding genes. CTX-M-2 and CTX-M-8 enzymes were found in Brazil in 1996, and two other CTX-M β-lactamases, CTX-M-9 and CTX-M-16, were subsequently observed. These reports are evidence of the diversity of CTX-M-type extended-spectrum β-lactamases in Brazil.

scholarly journals The molecular mechanisms underlying hidden phenotypic variation among metallo-ß-lactamases

2018 ◽  
Author(s):  
Raymond D. Socha ◽  
Nobuhiko Tokuriki
Keyword(s):  
Antibiotic Resistance ◽  
Genetic Variation ◽  
Gene Transfer ◽  
Phenotypic Variation ◽  
Functional Role ◽  
Molecular Mechanisms ◽  
Antibiotic Resistance Genes ◽  
Catalytic Efficiency ◽  
Orthologous Genes ◽  
Cellular Processes

AbstractGenetic variation among orthologous genes has been largely formed through neutral genetic drift to maintain the same functional role. In some circumstances, however, this genetic variation can create critical phenotypic variation, particularly when genes are transferred to a new host by horizontal gene transfer (HGT). Unveiling “hidden phenotypic variation” through HGT is especially important for genes that confer resistance to antibiotics, which continue to disseminate to new organisms through HGT. Despite this biomedical importance, our understanding of the molecular mechanisms that underlie hidden phenotypic variation remains limited. Here we sought to determine the extent of hidden phenotypic variation in the B1 metallo-β-lactamase (MBL) family, as well as to determine its molecular basis by systematically characterizing eight MBL orthologs when they are expressed in three different organisms (E. coli, P. aeruginosa, and K. pneumoniae). We found that these MBLs confer diverse levels of resistance in each organism, which cannot be explained by variation in catalytic efficiency alone; rather, it is the combination of the catalytic efficiency and abundance of functional periplasmic enzyme that best predicts the observed variation in resistance. The level of functional periplasmic expression varied dramatically between MBL orthologs and between hosts. This was the result changes at multiple levels of each enzyme’s functional: 1) the quantity of mRNA; 2) the amount of MBL expressed; and 3) the efficacy of functional enzyme translocation to the periplasm. Overall, we see that it is the interaction between each gene and the host’s underlying cellular processes (transcription, translation, and translocation) that determines MBL genetic incompatibility thorough HGT. These host-specific processes may constrain the effective spread and deployment of MBLs to certain host species, and could explain the current observed distribution bias.Author SummaryOrthologous genes spread among different organisms, typically maintaining the same functional role within the cell while accumulating some, presumably functionally-inert, genetic variation over time. However, these seemingly neutral gene sequence changes among orthologs can be revealed to have substantial difference in protein phenotypes, and thus, organismal fitness, when they are transferred to other host species. This so-called “hidden phenotypic variation” through horizontal gene transfer may play an important role in dissemination of antibiotic resistance genes, in particular. In this work, we systematically investigated the extent of phenotypic variation in eight orthologous antibiotic resistant genes from the metallo-β-lactamases family (MBLs), and identified the molecular causes underlying the observed phenotypic variation. We found that functional protein expression varied substantially among MBLs (causing significant variation in the level of antibiotic resistance conferred), and that this could not be explained by variation in catalytic efficiency alone. Instead, we see that functional variation is caused by multiple steps in the protein production, transcription, translation and translocation, that are necessary to provide functional enzymes in the bacterial periplasm. Thus, the successful gene transfer and dissemination of antibiotic resistance genes can be determined by complex interactions between the gene and host underlying cellular processes.

scholarly journals FKS1 Mutations Responsible for Selective Resistance of Saccharomyces cerevisiae to the Novel 1,3-β-Glucan Synthase Inhibitor Arborcandin C

2004 ◽  
Vol 48 (1) ◽  
pp. 319-322 ◽  
Author(s):  
Takao Ohyama ◽  
Shunichi Miyakoshi ◽  
Fujio Isono
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Amino Acid ◽  
Antifungal Activity ◽  
Amino Acid Replacement ◽  
Single Amino Acid ◽  
The Novel ◽  
Glucan Synthase ◽  
Synthase Inhibitor

ABSTRACT Arborcandin C is a novel antibiotic with potent antifungal activity that inhibits 1,3-β-glucan synthase in fungi. We examined spontaneous Saccharomyces cerevisiae mutants which are selectively resistant to arborcandin C and revealed that a single amino acid replacement in Fks1p of Asn470 with Lys or of Leu642 with Ser confers selective resistance on Fks1p mutants.

Deletion of a Conserved Regulatory Element in the Drosophila Adh Gene Leads to Increased Alcohol Dehydrogenase Activity but Also Delays Development

Genetics ◽  
2000 ◽  
Vol 156 (1) ◽  
pp. 219-227 ◽  
Author(s):  
John Parsch ◽  
Jacob A Russell ◽  
Isabel Beerman ◽  
Daniel L Hartl ◽  
Wolfgang Stephan
Keyword(s):  
Amino Acid ◽  
Alcohol Dehydrogenase ◽  
Enzymatic Activity ◽  
Regulatory Element ◽  
Catalytic Efficiency ◽  
Purifying Selection ◽  
Amino Acid Replacement ◽  
Detectable Effect ◽  
Twofold Increase

Abstract In vivo levels of enzymatic activity may be increased through either structural or regulatory changes. Here we use Drosophila melanogaster alcohol dehydrogenase (ADH) in an experimental test for selective differences between these two mechanisms. The well-known ADH-Slow (S)/Fast (F) amino acid replacement leads to a twofold increase in activity by increasing the catalytic efficiency of the enzyme. Disruption of a highly conserved, negative regulatory element in the Adh 3′ UTR also leads to a twofold increase in activity, although this is achieved by increasing in vivo Adh mRNA and protein concentrations. These two changes appear to be under different types of selection, with positive selection favoring the amino acid replacement and purifying selection maintaining the 3′ UTR sequence. Using transgenic experiments we show that deletion of the conserved 3′ UTR element increases adult and larval Adh expression in both the ADH-F and ADH-S genetic backgrounds. However, the 3′ UTR deletion also leads to a significant increase in developmental time in both backgrounds. ADH allozyme type has no detectable effect on development. These results demonstrate a negative fitness effect associated with Adh overexpression. This provides a mechanism whereby natural selection can discriminate between alternative pathways of increasing enzymatic activity.

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

scholarly journals Sequence Comparison of Vaginolysin from Different Gardnerella Species

Pathogens ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 86
Author(s):  
Erin M. Garcia ◽  
Myrna G. Serrano ◽  
Laahirie Edupuganti ◽  
David J. Edwards ◽  
Gregory A. Buck ◽  
...  
Keyword(s):  
Amino Acid ◽  
Human Microbiome ◽  
Human Microbiome Project ◽  
Distinct Species ◽  
Vaginal Swab ◽  
Metagenomic Data ◽  
Gardnerella Vaginalis ◽  
Vaginal Epithelial Cells ◽  
Species Specific

Gardnerella vaginalis has recently been split into 13 distinct species. In this study, we tested the hypotheses that species-specific variations in the vaginolysin (VLY) amino acid sequence could influence the interaction between the toxin and vaginal epithelial cells and that VLY variation may be one factor that distinguishes less virulent or commensal strains from more virulent strains. This was assessed by bioinformatic analyses of publicly available Gardnerella spp. sequences and quantification of cytotoxicity and cytokine production from purified, recombinantly produced versions of VLY. After identifying conserved differences that could distinguish distinct VLY types, we analyzed metagenomic data from a cohort of female subjects from the Vaginal Human Microbiome Project to investigate whether these different VLY types exhibited any significant associations with symptoms or Gardnerella spp.-relative abundance in vaginal swab samples. While Type 1 VLY was most prevalent among the subjects and may be associated with increased reports of symptoms, subjects with Type 2 VLY dominant profiles exhibited increased relative Gardnerella spp. abundance. Our findings suggest that amino acid differences alter the interaction of VLY with vaginal keratinocytes, which may potentiate differences in bacterial vaginosis (BV) immunopathology in vivo.

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