Paralogs of aminoacyl-tRNA synthetases

Aminoacil-tRNA-sintetaze ključni su enzimi u biosintetskom putu proteina i jedni od evolucijski najstarijih enzima. Analizama njima homolognih genskih sekvenci i proteinskih struktura utvrđeno je postojanje cijelog spektra tzv. krnjih paraloga, koji su funkcionalno uglavnom divergirali od svojih originala u više različitih smjerova. Ovim radom napravljen je osvrt na gotovo sve skupine otkrivenih paraloga te je izložena i komentirana funkcija, struktura i evolucija najzanimljivijih od njih. Paralozi su svrstani prema svojstvu homologije koju nose u dvije veće skupine, ovisno o tome sadrže li sekvencu homolognu katalitičkoj domeni odgovarajuće aaRS ili ne. Poseban je naglasak stavljen na nedavno otkrivene paraloge specifičnog metanogenog tipa seril-tRNA-sintetaza, čije su detaljne biokemijske i strukturalne analize upravo u tijeku.Aminoacyl-tRNA synthetases are one of the key enzymes in protein biosynthesis and one of the evolutionary oldest enzymes as well. By analyses of their homologic sequences and protein structures, the existance of a wide spectrum of socalled truncated paralogs, which have mostly functionaly diverged from their originals into several different new pathways, has been shown. In this work a critical review of almost all groups of determined paralogs has been made. Also, function, structure and evolution of the most interesting ones has been established and commented. Paralogs have been divided into two larger subgroups based on their homology characteristics, depending on the homologous catalytic domain possesion. A special emphasis has been put on recently discovered methanogenic seryl-tRNA synthetases paralogs, whose detailed biochemical and structural analyses have just been in progress

Paralogs of aminoacyl-tRNA synthetases

Aminoacil-tRNA-sintetaze ključni su enzimi u biosintetskom putu proteina i jedni od evolucijski najstarijih enzima. Analizama njima homolognih genskih sekvenci i proteinskih struktura utvrđeno je postojanje cijelog spektra tzv. krnjih paraloga, koji su funkcionalno uglavnom divergirali od svojih originala u više različitih smjerova. Ovim radom napravljen je osvrt na gotovo sve skupine otkrivenih paraloga te je izložena i komentirana funkcija, struktura i evolucija najzanimljivijih od njih. Paralozi su svrstani prema svojstvu homologije koju nose u dvije veće skupine, ovisno o tome sadrže li sekvencu homolognu katalitičkoj domeni odgovarajuće aaRS ili ne. Poseban je naglasak stavljen na nedavno otkrivene paraloge specifičnog metanogenog tipa seril-tRNA-sintetaza, čije su detaljne biokemijske i strukturalne analize upravo u tijeku.Aminoacyl-tRNA synthetases are one of the key enzymes in protein biosynthesis and one of the evolutionary oldest enzymes as well. By analyses of their homologic sequences and protein structures, the existance of a wide spectrum of socalled truncated paralogs, which have mostly functionaly diverged from their originals into several different new pathways, has been shown. In this work a critical review of almost all groups of determined paralogs has been made. Also, function, structure and evolution of the most interesting ones has been established and commented. Paralogs have been divided into two larger subgroups based on their homology characteristics, depending on the homologous catalytic domain possesion. A special emphasis has been put on recently discovered methanogenic seryl-tRNA synthetases paralogs, whose detailed biochemical and structural analyses have just been in progress

Paralogs of aminoacyl-tRNA synthetases

Aminoacil-tRNA-sintetaze ključni su enzimi u biosintetskom putu proteina i jedni od evolucijski najstarijih enzima. Analizama njima homolognih genskih sekvenci i proteinskih struktura utvrđeno je postojanje cijelog spektra tzv. krnjih paraloga, koji su funkcionalno uglavnom divergirali od svojih originala u više različitih smjerova. Ovim radom napravljen je osvrt na gotovo sve skupine otkrivenih paraloga te je izložena i komentirana funkcija, struktura i evolucija najzanimljivijih od njih. Paralozi su svrstani prema svojstvu homologije koju nose u dvije veće skupine, ovisno o tome sadrže li sekvencu homolognu katalitičkoj domeni odgovarajuće aaRS ili ne. Poseban je naglasak stavljen na nedavno otkrivene paraloge specifičnog metanogenog tipa seril-tRNA-sintetaza, čije su detaljne biokemijske i strukturalne analize upravo u tijeku.Aminoacyl-tRNA synthetases are one of the key enzymes in protein biosynthesis and one of the evolutionary oldest enzymes as well. By analyses of their homologic sequences and protein structures, the existance of a wide spectrum of socalled truncated paralogs, which have mostly functionaly diverged from their originals into several different new pathways, has been shown. In this work a critical review of almost all groups of determined paralogs has been made. Also, function, structure and evolution of the most interesting ones has been established and commented. Paralogs have been divided into two larger subgroups based on their homology characteristics, depending on the homologous catalytic domain possesion. A special emphasis has been put on recently discovered methanogenic seryl-tRNA synthetases paralogs, whose detailed biochemical and structural analyses have just been in progress

Precise optical control of gene expression in C elegans using improved genetic code expansion and Cre recombinase.

Synthetic strategies for optically controlling gene expression may enable the precise spatiotemporal control of genes in any combination of cells that cannot be targeted with specific promoters. We develop an improved genetic code expansion system in Caenorhabditis elegans and use it to create a photoactivatable Cre recombinase. We laser-activate Cre in single neurons within a bilaterally symmetric pair to selectively switch on expression of a loxP-controlled optogenetic channel in the targeted neuron. We use the system to dissect, in freely moving animals, the individual contributions of the mechanosensory neurons PLML/PLMR to the C. elegans touch response circuit, revealing distinct and synergistic roles for these neurons. We thus demonstrate how genetic code expansion and optical targeting can be combined to break the symmetry of neuron pairs and dissect behavioural outputs of individual neurons that cannot be genetically targeted

Efficient and Rapid <i>C. elegans</i> Transgenesis by Bombardment and Hygromycin B Selection

<div><p>We report a simple, cost-effective, scalable and efficient method for creating transgenic <i>Caenorhabditis elegans</i> that requires minimal hands-on time. The method combines biolistic bombardment with selection for transgenics that bear a hygromycin B resistance gene on agar plates supplemented with hygromycin B, taking advantage of our observation that hygromycin B is sufficient to kill wild-type <i>C. elegans</i> at very low concentrations. Crucially, the method provides substantial improvements in the success of bombardments for isolating transmitting strains, the isolation of multiple independent strains, and the isolation of integrated strains: 100% of bombardments in a large data set yielded transgenics; 10 or more independent strains were isolated from 84% of bombardments, and up to 28 independent strains were isolated from a single bombardment; 82% of bombardments yielded stably transmitting integrated lines with most yielding multiple integrated lines. We anticipate that the selection will be widely adopted for <i>C. elegans</i> transgenesis via bombardment, and that hygromycin B resistance will be adopted as a marker in other approaches for manipulating, introducing or deleting DNA in <i>C. elegans</i>.</p></div

Efficiency of biolistic <i>C. elegans</i> transgenesis using hygromycin B selection.

<p>n.d. – not determined.</p

Hygromycin B allows long term maintenance of non-integrated transgenes.

<p>a) 3 transgenic worms from a non-integrated line transformed with the hygromycin B resistance and GFP (P<i>rps-0</i>::<i>HygB</i>::<i>unc-54,</i> P<i>rps-0</i>::GFP::<i>unc-54</i>, bombardment 63, strain 63.1.2) were grown on a seeded plate for 3 generations in the absence and presence of hygromycin B. Worms were imaged as described in the methods section. Exposure time: 700 ms. b) Worms with a non-integrated transgenic array carrying the hygromycin B resistance gene and GFP (P<i>rps-0</i>::<i>HygB</i>::<i>unc-54,</i> P<i>rps-0</i>::GFP::<i>unc-54</i>, bombardment 30, strain 30.9.3) were propagated for >30 generations in the presence of hygromycin B. Worms were imaged as described in the methods section. Exposure time: 700 ms.</p

Hygromycin B independent transmission of integrated transgenes.

<p>Worms expressing the hygromycin B resistance gene and mCherry from the ubiquitous P<i>rps-0</i> promoter and GFP from the pan-neuronal P<i>snb-1</i> promoter (P<i>rps-0</i>::<i>HygB,</i> P<i>rps-0</i>::mCherry, P<i>snb-1</i>::<i>GFP</i>, bombardment 64, strain 64.1.1) were grown as described in Figure S3. Worms were washed off the plate and imaged using a confocal microscope as described in the methods section. The strain was grown and propagated in the absence of hygromycin B.</p

Survival of <i>C. elegans</i> in the presence of hygromycin B.

<p>a) 3000 synchronized L1 larvae were transferred to seeded 6 cm NGM plates and immediately treated with hygromycin B. Images of control and treated plates were acquired 40 hours later. b) Survival assay on hygromycin B dilution. 3000 synchronised L1 larvae were plated on seeded 6 cm plates and immediately treated with hygromycin B at the specified final concentrations. The plates were scored for L4 larvae after 40 hours and for adults after 90 hours. The experiment was performed in triplicate, error bars represent standard deviation. c) Selection of transgenic animals on hygromycin B. 10 synchronized L1 larvae carrying a hygromycin B resistance gene and expressing GFP/mCherry were mixed with the indicated number of wild type L1 larvae on a seeded 6 cm plate and immediately treated with hygromycin B (0.3 mg ml⁻¹). The number of adult transgenic (fluorescence-positive) and non-transgenic (fluorescence-negative) animals was scored after 90 hours. The experiment was performed with two independent hygromycin B resistant transgenic strains.</p

Hygromycin B selection of transgenic <i>C. elegans</i> created by biolistic bombardment.

<p>Gold beads coated with the DNA mixture of interest, carrying the hygromycin B resistance gene, are bombarded onto worms spread on an agar plate. Bombarded worms are split onto 10–20 selection plates and left to lay eggs for 2–3 days, at which point hygromycin B is added to the plates. After 4–7 days surviving transgenic worms can be picked.</p