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Putative Homologs (putative + homolog)
Selected AbstractsThe Legionella pneumophila Dps homolog is regulated by iron and involved in multiple stress toleranceJOURNAL OF BASIC MICROBIOLOGY, Issue S1 2009Ming-jia Yu Abstract Iron homeostasis is essential to almost all organisms. In this study, we identified the putative homolog of the iron-storage protein-encoding gene, dpsL, in the intracellular pathogen Legionella pneumophila and demonstrated its expression under iron-limited conditions and its responses to multiple stresses. Quantitative real-time PCR analysis indicated that the expression of dpsL was enhanced under iron limitation regardless of the growth phase. Compared with the wild-type cells, the cells devoid of dpsL were heat and H2O2 -sensitive. In contrast to the dps mutants of other bacteria, the growth of the dpsL mutant in an iron-deprived medium was delayed but finally reached the same cell density as wild-type cells during the stationary phase of growth. The finding that the dpsL mutant is salt resistant suggested the involvement of DpsL in virulence. (© 2009 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Efficient recognition of protein fold at low sequence identity by conservative application of Psi-BLAST: validation,JOURNAL OF MOLECULAR RECOGNITION, Issue 2 2005F. J. Stevens Abstract A substantial fraction of protein sequences derived from genomic analyses is currently classified as representing ,hypothetical proteins of unknown function'. In part, this reflects the limitations of methods for comparison of sequences with very low identity. We evaluated the effectiveness of a Psi-BLAST search strategy to identify proteins of similar fold at low sequence identity. Psi-BLAST searches for structurally characterized low-sequence-identity matches were carried out on a set of over 300 proteins of known structure. Searches were conducted in NCBI's non-redundant database and were limited to three rounds. Some 614 potential homologs with 25% or lower sequence identity to 166 members of the search set were obtained. Disregarding the expect value, level of sequence identity and span of alignment, correspondence of fold between the target and potential homolog was found in more than 95% of the Psi-BLAST matches. Restrictions on expect value or span of alignment improved the false positive rate at the expense of eliminating many true homologs. Approximately three-quarters of the putative homologs obtained by three rounds of Psi-BLAST revealed no significant sequence similarity to the target protein upon direct sequence comparison by BLAST, and therefore could not be found by a conventional search. Although three rounds of Psi-BLAST identified many more homologs than a standard BLAST search, most homologs were undetected. It appears that more than 80% of all homologs to a target protein may be characterized by a lack of significant sequence similarity. We suggest that conservative use of Psi-BLAST has the potential to propose experimentally testable functions for the majority of proteins currently annotated as ,hypothetical proteins of unknown function';. Copyright © 2004 John Wiley & Sons, Ltd. [source] The pars intercerebralis of the locust brain: A developmental and comparative studyMICROSCOPY RESEARCH AND TECHNIQUE, Issue 3 2002Peter Ludwig Abstract The anterior midline of the brain, also known as the pars intercerebralis, contains the largest collection of neurosecretory cells in the central nervous system of the grasshopper. In this study, we use immunocytochemical, intracellular staining, and histological methods to establish the ontogenies of the various cell types in the brain midline, and show how these cells contribute to the pars intercerebralis of the adult brain. We show that the adult pars intercerebralis develops from three distinct embryonic cell groups: (1) the median neurosecretory cells, which derive from a subset of neuroblasts in the protocerebral hemispheres, and which project axons to the corpora cardiaca; (2) the paired primary commissure pioneers, which derive directly from the mesectoderm of the dorsal median domain and whose axons project to the ventral nerve cord via the midline tract; and (3) the six progeny of the median precursor in the dorsal median domain, which share a common axonal projection with the primary commissure pioneers. Since the adult pars intercerebralis is a fusion product of these independent cellular components, it can only be understood in terms of its origins in the embryonic brain. When the expression pattern of the TERM-1 antigen is compared in subsets of median neurosecretory cells in a wide range of insect orders, the results suggests a common organizational Bauplan for the pars intercerebralis. This hypothesis is supported by the identification of putative homologs of the grasshopper primary commissure pioneers in all these insects. Microsc. Res. Tech. 56:174,188, 2002. © 2002 Wiley-Liss, Inc. [source] Ice recrystallization inhibition proteins (IRIPs) and freeze tolerance in the cryophilic Antarctic hair grass Deschampsia antarctica E. Desv.PLANT CELL & ENVIRONMENT, Issue 4 2009ULRIK P. JOHN ABSTRACT Antarctic hair grass (Deschampsia antarctica E. Desv.), the only grass indigenous to Antarctica, has well-developed freezing tolerance, strongly induced by cold acclimation. Here, we show that in response to low temperatures, D. antarctica expresses potent recrystallization inhibition (RI) activity that, inhibits the growth of small ice crystals into potentially damaging large ones, is proteinaceous and localized to the apoplasm. A gene family from D. antarctica encoding putative homologs of an ice recrystallization inhibition protein (IRIP) has been isolated and characterized. IRIPs are apoplastically targeted proteins with two potential ice-binding motifs: 1,9 leucine-rich repeats (LRRs) and c. 16 ,IRIP' repeats. IRIP genes appear to be confined to the grass subfamily Pooideae and their products, exhibit sequence similarity to phytosulphokine receptors and are predicted to adopt conformations with two ice-binding surfaces. D. antarctica IRIP (DaIRIP) transcript levels are greatly enhanced in leaf tissue following cold acclimation. Transgenic Arabidopsis thaliana expressing a DaIRIP has novel RI activity, and purified DaIRIP, when added back to extracts of leaves from non-acclimated D. antarctica, can reconstitute the activity found in acclimated plants. We propose that IRIP-mediated RI activity may contribute to the cryotolerance of D. antarctica, and thus to its unique ability to have colonized Antarctica. [source] | ||||||||||