Lysine is an essential amino acid that is synthesized in plants and microorganisms via two metabo... more Lysine is an essential amino acid that is synthesized in plants and microorganisms via two metabolic routes which evolved independently. Fungi and some archaeal species employ the intermediate α-aminoadipate to anabolize lysine. Bacteria and photosynthetic cohorts, in contrast, employ the intermediate diaminopimelate. The biosynthesis of lysine is of continued interest, because animals do not possess the enzymatic machinery to mediate its synthesis. As such, lysine is deemed essential for humans, as it is one of the 20 ubiquitous proteogenic amino acids that must be acquired through dietary means to facilitate protein synthesis for growth and development. From an antimicrobial drug development perspective, the pathway is of interest given its involvement in the synthesis of the bacterial peptidoglycan cell wall. The penultimate compound, meso-diaminopimelate, serves as the cross-linking amino acid in the cell wall of most Gram-negative bacteria, while lysine serves the same purpose in the cell wall of most Gram-positive bacteria. The enzymes are therefore attractive targets for biocides (antibacterials, algicides and herbicides). The overarching goal of this chapter is to present an updated review of the various pathways for the synthesis of lysine. The α-aminoadipate pathway will only be briefly discussed, whereas an in-depth description of the four variants of the diaminopimelate pathways is included. In addition, structure-activity relationships and kinetic analyses of key steps involved in the pathways will also be featured.
Here, we report the genome assemblies of 11 endophytic bacteria, isolated from poison ivy vine ( ... more Here, we report the genome assemblies of 11 endophytic bacteria, isolated from poison ivy vine ( Toxicodendron radicans ). Five species belonging to the genus Pseudomonas , two species of Curtobacterium , one strain of Pantoea agglomerans , and one species from the Bacillus , Cellulomonas , and Enterobacter genera were isolated from the interior tissue of poison ivy.
Objectives To characterize the bacterial community of Wind Cave’s Madison aquifer through whole-g... more Objectives To characterize the bacterial community of Wind Cave’s Madison aquifer through whole-genome sequencing, and to better understand the bacterial ecology by identifying genes involved in acyl-homoserine lactone (AHL) based quorum-sensing (QS) systems. Results Genome-based taxonomic classification revealed the microbial richness present in the pristine Madison aquifer. The strains were found to span eleven genera and fourteen species, of which eight had uncertain taxonomic classifications. The genomes of strains SD129 and SD340 were found to contain the archetypical AHL QS system composed of two genes, luxI and luxR. Surprisingly, the genomes of strains SD115, SD129, SD274 and SD316 were found to contain one to three luxR orphans (solos). Strain SD129, besides possessing an archetypical AHL QS luxI-luxR pair, also contained two luxR solos, while strain SD316 contained three LuxR solos and no luxI-luxR pairs. The ligand-binding domain of two LuxR solos, one each from strains S...
Genomic resources remain scarce for bacteria isolated from oligotrophic caves. We sequenced the g... more Genomic resources remain scarce for bacteria isolated from oligotrophic caves. We sequenced the genomes of five proteobacteria isolated from Lechuguilla Cave in New Mexico, USA. Genome-based phylogeny indicates that each strain belongs to a distinct genus. Two Rhizobiaceae isolates possess the genomic potential for the biosynthesis of acyl-homoserine lactone.
Here, we report the whole-genome sequences and annotation of 11 endophytic bacteria from poison i... more Here, we report the whole-genome sequences and annotation of 11 endophytic bacteria from poison ivy (Toxicodendron radicans) vine tissue. Five bacteria belong to the genus Pseudomonas, and six single members from other genera were found present in interior vine tissue of poison ivy.
Current topics in microbiology and immunology, 2018
This chapter presents a historical overview of the development and changes in scientific approach... more This chapter presents a historical overview of the development and changes in scientific approaches to classifying members of the Agrobacterium genus. We also describe the changes in the inference of evolutionary relationships among Agrobacterium biovars and Agrobacterium strains from using the 16S rRNA marker to recA genes and to the use of multilocus sequence analysis (MLSA). Further, the impacts of the genomic era enabling low cost and rapid whole genome sequencing on Agrobacterium phylogeny are reviewed with a focus on the use of new and sophisticated bioinformatics approaches to refine phylogenetic inferences. An updated genome-based phylogeny of ninety-seven Agrobacterium tumefaciens complex isolates representing ten known genomic species is presented, providing additional support to the monophyly of the Agrobacterium clade. Additional taxon sampling within Agrobacterium genomovar G3 indicates potential exceptions to interpretation of the concept of bacterial genomics species ...
To test the hypothesis that auxin-binding protein 1 (ABP1) is a receptor controlling auxin-mediat... more To test the hypothesis that auxin-binding protein 1 (ABP1) is a receptor controlling auxin-mediated plant cell expansion, ABP1 complementary DNAs were expressed in a controllable fashion in tobacco plants and constitutively in maize cell lines. Induction of Arabidopsis ABP1 expression in tobacco leaf strips resulted in an increased capacity for auxin-mediated cell expansion, whereas induction of ABP1 in intact plants resulted in leaves with a normal morphology, but larger cells. Similarly, constitutive expression of maize ABP1 in maize cell lines conferred on them the capacity to respond to auxin by increasing cell size. These results support a role of ABP1 as an auxin receptor controlling plant growth.
Lysine is an essential amino acid that is synthesized in plants and microorganisms via two metabo... more Lysine is an essential amino acid that is synthesized in plants and microorganisms via two metabolic routes which evolved independently. Fungi and some archaeal species employ the intermediate α-aminoadipate to anabolize lysine. Bacteria and photosynthetic cohorts, in contrast, employ the intermediate diaminopimelate. The biosynthesis of lysine is of continued interest, because animals do not possess the enzymatic machinery to mediate its synthesis. As such, lysine is deemed essential for humans, as it is one of the 20 ubiquitous proteogenic amino acids that must be acquired through dietary means to facilitate protein synthesis for growth and development. From an antimicrobial drug development perspective, the pathway is of interest given its involvement in the synthesis of the bacterial peptidoglycan cell wall. The penultimate compound, meso-diaminopimelate, serves as the cross-linking amino acid in the cell wall of most Gram-negative bacteria, while lysine serves the same purpose in the cell wall of most Gram-positive bacteria. The enzymes are therefore attractive targets for biocides (antibacterials, algicides and herbicides). The overarching goal of this chapter is to present an updated review of the various pathways for the synthesis of lysine. The α-aminoadipate pathway will only be briefly discussed, whereas an in-depth description of the four variants of the diaminopimelate pathways is included. In addition, structure-activity relationships and kinetic analyses of key steps involved in the pathways will also be featured.
Here, we report the genome assemblies of 11 endophytic bacteria, isolated from poison ivy vine ( ... more Here, we report the genome assemblies of 11 endophytic bacteria, isolated from poison ivy vine ( Toxicodendron radicans ). Five species belonging to the genus Pseudomonas , two species of Curtobacterium , one strain of Pantoea agglomerans , and one species from the Bacillus , Cellulomonas , and Enterobacter genera were isolated from the interior tissue of poison ivy.
Objectives To characterize the bacterial community of Wind Cave’s Madison aquifer through whole-g... more Objectives To characterize the bacterial community of Wind Cave’s Madison aquifer through whole-genome sequencing, and to better understand the bacterial ecology by identifying genes involved in acyl-homoserine lactone (AHL) based quorum-sensing (QS) systems. Results Genome-based taxonomic classification revealed the microbial richness present in the pristine Madison aquifer. The strains were found to span eleven genera and fourteen species, of which eight had uncertain taxonomic classifications. The genomes of strains SD129 and SD340 were found to contain the archetypical AHL QS system composed of two genes, luxI and luxR. Surprisingly, the genomes of strains SD115, SD129, SD274 and SD316 were found to contain one to three luxR orphans (solos). Strain SD129, besides possessing an archetypical AHL QS luxI-luxR pair, also contained two luxR solos, while strain SD316 contained three LuxR solos and no luxI-luxR pairs. The ligand-binding domain of two LuxR solos, one each from strains S...
Genomic resources remain scarce for bacteria isolated from oligotrophic caves. We sequenced the g... more Genomic resources remain scarce for bacteria isolated from oligotrophic caves. We sequenced the genomes of five proteobacteria isolated from Lechuguilla Cave in New Mexico, USA. Genome-based phylogeny indicates that each strain belongs to a distinct genus. Two Rhizobiaceae isolates possess the genomic potential for the biosynthesis of acyl-homoserine lactone.
Here, we report the whole-genome sequences and annotation of 11 endophytic bacteria from poison i... more Here, we report the whole-genome sequences and annotation of 11 endophytic bacteria from poison ivy (Toxicodendron radicans) vine tissue. Five bacteria belong to the genus Pseudomonas, and six single members from other genera were found present in interior vine tissue of poison ivy.
Current topics in microbiology and immunology, 2018
This chapter presents a historical overview of the development and changes in scientific approach... more This chapter presents a historical overview of the development and changes in scientific approaches to classifying members of the Agrobacterium genus. We also describe the changes in the inference of evolutionary relationships among Agrobacterium biovars and Agrobacterium strains from using the 16S rRNA marker to recA genes and to the use of multilocus sequence analysis (MLSA). Further, the impacts of the genomic era enabling low cost and rapid whole genome sequencing on Agrobacterium phylogeny are reviewed with a focus on the use of new and sophisticated bioinformatics approaches to refine phylogenetic inferences. An updated genome-based phylogeny of ninety-seven Agrobacterium tumefaciens complex isolates representing ten known genomic species is presented, providing additional support to the monophyly of the Agrobacterium clade. Additional taxon sampling within Agrobacterium genomovar G3 indicates potential exceptions to interpretation of the concept of bacterial genomics species ...
To test the hypothesis that auxin-binding protein 1 (ABP1) is a receptor controlling auxin-mediat... more To test the hypothesis that auxin-binding protein 1 (ABP1) is a receptor controlling auxin-mediated plant cell expansion, ABP1 complementary DNAs were expressed in a controllable fashion in tobacco plants and constitutively in maize cell lines. Induction of Arabidopsis ABP1 expression in tobacco leaf strips resulted in an increased capacity for auxin-mediated cell expansion, whereas induction of ABP1 in intact plants resulted in leaves with a normal morphology, but larger cells. Similarly, constitutive expression of maize ABP1 in maize cell lines conferred on them the capacity to respond to auxin by increasing cell size. These results support a role of ABP1 as an auxin receptor controlling plant growth.
Uploads
Papers by Michael Savka