Pathogenic and molecular detection of Fusarium oxysporum f. sp. albedinis isolates from different areas in southwest Algeria

Purpose: To investigate the intra-specific variations in eleven Fusarium oxysporum isolates from infected date palm using pathogenicity and molecular methods.Methods: Eleven isolates of Fusarium oxysporum obtained from infected date palms in the south-west region of Algeria were subjected to confirmatory test using a specific polymerase chain reaction (PCR) technique with the primer pairs, TL3-FOA28 and BIO3-FOA1. Polymorphism in the 5’ domain of the large subunit rRNA was investigated. Small libraries of the domain, amplified by the primer pair, LR3/LROR, were constructed and the inserts sequenced.Results: The 11 isolates of Fusarium oxysporum collected from the infected date palm were confirmed as Fusarium oxysporun f. sp albedinis. Results from the investigation of polymorphism in the 5’ domain of the large subunit rRNA revealed that the sequences were 100 % homologous or extremely close (> 99.4 %, differing by no more than one to three nucleotides) to several Fusarium oxysporum sequences. In addition, F. inflexum (U34548.1) was highly homologous to one of the F. oxysporum f. sp. albedinis.Conclusion: The sequences of the 11 isolates are almost 100 % homologous to several F. oxysporum species. It is noteworthy that a sequence highly homologous to one of the F. oxysporum f. sp. albedinis is obtainable from a different species, F. inflexum (U34548.1).Keywords:  Fusarium oxysporum f. sp. albedinis, Date palm, rRNA gene polymorphis

Antimicrobial properties of Pseudomonas strains producing the antibiotic mupirocin

peer reviewe

Retrieving sequences of enzymes experimentally characterized but erroneously annotated : the case of the putrescine carbamoyltransferase

BACKGROUND: Annotating genomes remains an hazardous task. Mistakes or gaps in such a complex process may occur when relevant knowledge is ignored, whether lost, forgotten or overlooked. This paper exemplifies an approach which could help to ressucitate such meaningful data. RESULTS: We show that a set of closely related sequences which have been annotated as ornithine carbamoyltransferases are actually putrescine carbamoyltransferases. This demonstration is based on the following points : (i) use of enzymatic data which had been overlooked, (ii) rediscovery of a short NH(2)-terminal sequence allowing to reannotate a wrongly annotated ornithine carbamoyltransferase as a putrescine carbamoyltransferase, (iii) identification of conserved motifs allowing to distinguish unambiguously between the two kinds of carbamoyltransferases, and (iv) comparative study of the gene context of these different sequences. CONCLUSIONS: We explain why this specific case of misannotation had not yet been described and draw attention to the fact that analogous instances must be rather frequent. We urge to be especially cautious when high sequence similarity is coupled with an apparent lack of biochemical information. Moreover, from the point of view of genome annotation, proteins which have been studied experimentally but are not correlated with sequence data in current databases qualify as "orphans", just as unassigned genomic open reading frames do. The strategy we used in this paper to bridge such gaps in knowledge could work whenever it is possible to collect a body of facts about experimental data, homology, unnoticed sequence data, and accurate informations about gene context

New Insight into the Transcarbamylase Family: The Structure of Putrescine Transcarbamylase, a Key Catalyst for Fermentative Utilization of Agmatine

Transcarbamylases reversibly transfer a carbamyl group from carbamylphosphate (CP) to an amine. Although aspartate transcarbamylase and ornithine transcarbamylase (OTC) are well characterized, little was known about putrescine transcarbamylase (PTC), the enzyme that generates CP for ATP production in the fermentative catabolism of agmatine. We demonstrate that PTC (from Enterococcus faecalis), in addition to using putrescine, can utilize L-ornithine as a poor substrate. Crystal structures at 2.5 Å and 2.0 Å resolutions of PTC bound to its respective bisubstrate analog inhibitors for putrescine and ornithine use, N-(phosphonoacetyl)-putrescine and δ-N-(phosphonoacetyl)-L-ornithine, shed light on PTC preference for putrescine. Except for a highly prominent C-terminal helix that projects away and embraces an adjacent subunit, PTC closely resembles OTCs, suggesting recent divergence of the two enzymes. Since differences between the respective 230 and SMG loops of PTC and OTC appeared to account for the differential preference of these enzymes for putrescine and ornithine, we engineered the 230-loop of PTC to make it to resemble the SMG loop of OTCs, increasing the activity with ornithine and greatly decreasing the activity with putrescine. We also examined the role of the C-terminal helix that appears a constant and exclusive PTC trait. The enzyme lacking this helix remained active but the PTC trimer stability appeared decreased, since some of the enzyme eluted as monomers from a gel filtration column. In addition, truncated PTC tended to aggregate to hexamers, as shown both chromatographically and by X-ray crystallography. Therefore, the extra C-terminal helix plays a dual role: it stabilizes the PTC trimer and, by shielding helix 1 of an adjacent subunit, it prevents the supratrimeric oligomerizations of obscure significance observed with some OTCs. Guided by the structural data we identify signature traits that permit easy and unambiguous annotation of PTC sequences

La dégradation de l'arginine, en aérobiose et en anaérobiose, chez les pseudomonas

Doctorat en Sciencesinfo:eu-repo/semantics/nonPublishe

La dégradation de l'arginine, en aérobiose et en anaérobiose, chez les pseudomonas

Doctorat en Sciencesinfo:eu-repo/semantics/nonPublishe

Purification of ArcR, an oxidation-sensitive regulatory protein from Bacillus licheniformis

In Bacillus licheniformis, ArcR, a transcriptional activator of the Crp/Fnr family, is required for expression of the anaerobic pathway of arginine catabolism, the arginine deiminase pathway. The method described here allows the purification of milligram quantities of functional ArcR from a recombinant Escherichia coli strain. The solubility properties of ArcR were much exploited during the purification process. The protein appeared highly sensitive to oxidation. Oxidation-induced precipitation of the protein was attributed to the formation of intermolecular disulfide bridges. Alkylation of mutant proteins with single substitutions showed that both cysteine residues of the protein, C178 and C205, are involved in formation of the disulfide bridges. Substitution of both cysteines yielded a functional protein insensitive to oxidation and able to form a complex with its cognate target on the DNA. © 2004 Elsevier Inc. All rights reserved.SCOPUS: ar.jinfo:eu-repo/semantics/publishe

Biodegradation of polycaprolactone by micro-organisms from an industrial compost of household refuse

SCOPUS: ar.jinfo:eu-repo/semantics/publishe