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Title: Structural analysis and profiling of phenolic secondary metabolites of Mexican lupine species using LC-MS techniques
Author: Zhang, M.
Putonti, C.
Chumakov, S.
Gupta, A.
Fox, G.E.
Graur, D.
Fofanov, Y.
Issue Date: 2006
Abstract: Numerous sequencing projects have unveiled partial and full microbial genomes. The data produced far exceeds one person's analytical capabilities and thus requires the power of computing. A significant amount of work has focused on the diversity of statistical characteristics along microbial genomic sequences, e.g. codon bias, G+C content, the frequencies of short subsequences (n-mers), etc. Based upon the results of these studies, two observations were made: (1) there exists a correlation between regions of unusual statistical properties, e.g. difference in codon bias, etc., from the rest of the genomic sequence, and evolutionary significant regions, e.g. regions of horizontal gene transfer; and (2) because no two microbial genomes look statistically identical, statistical properties can be used to distinguish between genomic sequences. Recently, we conducted extensive analysis on the presence/absence of n-mers for many microbial genomes as well as several viral and eukaryotic genomes. This analysis revealed that the presence of n-mers in all genomes considered (in the range of n, when the condition M<<4n holds, where M is the genome length) can be treated as a nearly random and independent process. Thus we hypothesize that one may use relatively small sets of randomly picked n-mers for differentiating between different microorganisms. Recently, we analyzed the frequency of appearance of all 8- to 12-mers present in each of the 200+ publicly available microbial genomes. For nearly all of the genomes under consideration, we observed that some n-mers are present much more frequently than expected: from 50 to over a thousand copies. Upon closer inspection of these sequences, we found several cases in which an overrepresented n-mer exhibits a bias towards being located in the coding or being located in the non-coding region. Although the evolutionary reason for the conservation of such sequences remains unclear, in some cases it is plausible to believe that sequences having a clear bias for non-coding regions may be because of their role in the DNA uptake/recombination process, being parts in insertion sequences, or serving as transcription factors recognition sites. Our analysis of the frequency of appearance of 6-mers for each microbial genome revealed regions that display unusual statistical properties with respect to their own genome. After inspection of the genes contained within these regions, we believe that such regions are likely to have been acquired into the genomic sequence through horizontal gene transfer. " 2006 American Institute of Physics.",,,,,,"10.1063/1.2356390",,,"","",,,,,,,,"AIP Conference Proceedings",,"13
18",,"854",,"Scopus",,,,,,"Pathogen identification; Short subsequences; Statistical properties",,,,,,"Statistical properties of short subsequences in microbial genomes and their link to pathogen identification and evolution",,"Conference Paper" "46556","123456789/35008",,"Wojakowska, A., Institute of Bioorganic Chemistry PAS, Noskowskiego 12/14, 61-704 Poznan', Poland; Piasecka, A., Institute of Plant Genetics PAS, Strzeszyn'ska 34, 60-479 Poznan', Poland; García-López, P.M., Laboratory of Biotechnology, Department of Botany and Zoology, University of Guadalajara Las Agujas Nextipac, Zapopan Jalisco, Mexico; Zamora-Natera, F., Laboratory of Biotechnology, Department of Botany and Zoology, University of Guadalajara Las Agujas Nextipac, Zapopan Jalisco, Mexico; Krajewski, P., Institute of Plant Genetics PAS, Strzeszyn'ska 34, 60-479 Poznan', Poland; Marczak, ?., Institute of Bioorganic Chemistry PAS, Noskowskiego 12/14, 61-704 Poznan', Poland; Kachlicki, P., Institute of Plant Genetics PAS, Strzeszyn'ska 34, 60-479 Poznan', Poland; Stobiecki, M., Institute of Bioorganic Chemistry PAS, Noskowskiego 12/14, 61-704 Poznan', Poland",,"Wojakowska, A.
Piasecka, A.
García-Lopez, P.M.
Zamora-Natera, F.
Krajewski, P.
Marczak, L.
Kachlicki, P.
Stobiecki, M.",,"2013",,"Flavonoid glycoconjugates from roots and leaves of eight North America lupine species (Lupinus elegans, Lupinus exaltatus, Lupinus hintonii, Lupinus mexicanus, Lupinus montanus, Lupinus rotundiflorus, Lupinus stipulatus, Lupinus sp.), three Mediterranean species (Lupinus albus, Lupinus angustifolius, Lupinus luteus) and one species from South America domesticated in Europe (Lupinus mutabilis) were analyzed using two LC/MS systems: low-resolution ion trap instrument and high-resolution quadrupole-time-of-flight spectrometer. As a result of the LC/MS profiling using the CID/MSn experiments structures of 175 flavonoid glycoconjugates found in 12 lupine species were identified at three confidence levels according to the Metabolomic Standard Initiative, mainly at level 2 and 3, some of them were classified to the level 1. Among the flavonoid derivatives recognized in the plant extracts were isomeric or isobaric compounds, differing in the degree of hydroxylation of the aglycones and the presence of glycosidic, acyl or alkyl groups in the molecules. The elemental composition of the glycoconjugate molecules was established from the exact m/z values of the protonated/deprotonated molecules ([M+H] +/[M-H]-) measured with the accuracy better than 5 ppm. Information concerning structures of the aglycones, the type of sugar moieties (hexose, deoxyhexose or pentose) and, in some cases, their placement on the aglycones as well as the acyl substituents of the flavonoid glycoconjugates was achieved in experiments, in which collisioninduced dissociation was applied. Flavonoid aglycones present in the studied O-glycoconjugates were unambiguously identified after the comparison of the pseudo-MS3 spectra with the spectra registered for the standards. Isomers of flavonoid glycoconjugates, in which one or two sugar moieties were attached to 40- or 7-hydroxyl groups or directly to the C-6 or C-8 of the aglycones, could be distinguished on the basis of the MS2 spectra. However, the collision energy applied in the CID experiments had to be optimized for each group of the compounds and there were no universal settings that allowed the acquisition of structural information for all the compounds present in the sample. Information obtained from the flavonoid conjugate profiling was used for the chemotaxonomic comparison of the studied lupine species. A clear-cut discrimination of the Mediterranean and North American lupines was obtained as a result of this analysis. " 2013 Elsevier Ltd. All rights reserved.
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