Identification of putative exported/secreted proteins in prokaryotic proteomes

Saleh, Mazen; Fillon, Manuel; Brennan, Patrick J.; Belisle, John T.

doi:10.1016/s0378-1119(01)00436-x

Cited by 46 publications

(39 citation statements)

References 25 publications

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“…Descriptions of archaeal signal sequences have largely relied on analysis of genome sequences, using computer-based tools originally designed to detect eucaryal or bacterial signal sequences (2,16,35,94,306,371,377). At best, these algorithms should be able to identify only those archaeal signal sequences bearing sufficient similarity to their eucaryal and bacterial counterparts.…”

Section: Archaeal Signal Sequencesmentioning

confidence: 99%

Posttranslational Protein Modification inArchaea

Eichler

Adams

2005

Microbiol Mol Biol Rev

194

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One of the first hurdles to be negotiated in the postgenomic era involves the description of the entire protein content of the cell, the proteome. Such efforts are presently complicated by the various posttranslational modifications that proteins can experience, including glycosylation, lipid attachment, phosphorylation, methylation, disulfide bond formation, and proteolytic cleavage. Whereas these and other posttranslational protein modifications have been well characterized in Eucarya and Bacteria, posttranslational modification in Archaea has received far less attention. Although archaeal proteins can undergo posttranslational modifications reminiscent of what their eucaryal and bacterial counterparts experience, examination of archaeal posttranslational modification often reveals aspects not previously observed in the other two domains of life. In some cases, posttranslational modification allows a protein to survive the extreme conditions often encountered by Archaea. The various posttranslational modifications experienced by archaeal proteins, the molecular steps leading to these modifications, and the role played by posttranslational modification in Archaea form the focus of this review

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Section: Archaeal Signal Sequencesmentioning

confidence: 99%

Posttranslational Protein Modification inArchaea

Eichler

Adams

2005

Microbiol Mol Biol Rev

194

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“…tuberculosis has a unique cell wall consisting of three major structures: the cytoplasmic membrane, the cell wall core that contains peptidoglycan covalently linked to a highly branched heteropolysaccharide, and an outer lipid layer composed of a wide range of complex free lipids and forms a pseudo-bilayer with the mycolic acids, characteristics of the cell walls of both Grampositive and Gram-negative bacteria [4]. M. tuberculosis secreted proteins show typical signal sequences, but these are not present in CFP-10 [44]. Hence, it is unlikely that its N-terminus is cleaved (D 7 -Y 100 , R 57 -F 100 , Table 1) during Sec-dependent translocation.…”

Section: Secretary Modificationsmentioning

confidence: 99%

Top down characterization of secreted proteins from Mycobacterium tuberculosis by electron capture dissociation mass spectrometry

ElNaggar

Sze

et al. 2003

J. Am. Soc. Mass Spectrom.

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Secreted proteins of Mycobacterium tuberculosis are implicated in its disease pathogenesis and so are considered as potential diagnostic and vaccine candidates. The search for these has been slow, even though the entire genome sequence of M. tuberculosis is now available; of the 620 protein spots resolved by 2-D gel electrophoresis, 114 secreted proteins have been identified, but for only 13 has the primary structure been partly characterized. For comparison, in this top down mass spectrometry (MS) approach the secreted proteins were precipitated from cell culture filtrate, resuspended, and examined directly by electrospray ionization (ESI) Fourier transform MS. The ESI spectra of three precipitates showed 93, 535, and 369 molecular weight (M r ) values, for a total of 689 different values. However, only ϳ10% of these values matched (Ϯ1 Da) the DNA predicted M r values, but these identifications were unreliable. Of nine molecular ions characterized by MS/MS, only one protein match was confirmed, and its isotopic molecular ions were overlapped by those of another protein. MS/MS identified a total of ten proteins by sequence tag search, of which three were unidentified previously. The low success of M r matching was due to unusually extensive posttranslational modifications, including loss of a signal sequence, loss of the N-terminal residue, proteolytic degradation, oxidation, and glycosylation. Although in eubacteria the latter is relatively rare, a 9 kDa protein showed 7 hexose attachments and two 20 kDa proteins each had 20 attachments. For MS/MS, electron capture dissociation was especially effective. (J Am Soc Mass Spectrom 2003, 14, 253-261)

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“…Since the genome sequence of L. reuteri is not available, the number of proteins with N-terminal signal sequences encoded by this organism is unknown. By comparison with the relationship between genome size and number of extracellular proteins of other Gram-positive bacteria (Bolotin et al, 2001;Kleerebezem et al, 2003;Saleh et al, 2001), L. reuteri could be estimated to encode approximately 100-200 extracellular proteins. After sequencing 263 clones, 36 putative extracellular proteins of L. reuteri were identified in this study.…”

Section: First Panning Repanningmentioning

confidence: 99%

Phage display reveals 52 novel extracellular and transmembrane proteins from Lactobacillus reuteri DSM 20016T

et al. 2003

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Extracellular and transmembrane proteins are important for the binding of bacteria to intestinal surfaces and for their interaction with the host. The aim of this study was to identify genes encoding extracellular and transmembrane proteins from the probiotic bacterium Lactobacillus reuteri by construction and screening of a phage display library. This library was constructed by insertion of randomly fragmented DNA from L. reuteri into the phagemid vector pG3DSS, which was previously developed for screening for extracellular proteins. After affinity selection of the library, the L. reuteri inserts were sequenced and analysed with bioinformatic tools. The screening resulted in the identification of 52 novel genes encoding extracellular and transmembrane proteins. These proteins were classified as: transport proteins; enzymes; sensor-regulator proteins; proteins involved in host/microbial interactions; conserved hypothetical proteins; and unconserved hypothetical proteins. Further characterization of the extracellular and transmembrane proteins identified should contribute to the understanding of the probiotic properties of L. reuteri.

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Identification of putative exported/secreted proteins in prokaryotic proteomes

Cited by 46 publications

References 25 publications

Posttranslational Protein Modification inArchaea

Posttranslational Protein Modification inArchaea

Top down characterization of secreted proteins from Mycobacterium tuberculosis by electron capture dissociation mass spectrometry

Phage display reveals 52 novel extracellular and transmembrane proteins from Lactobacillus reuteri DSM 20016T

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