Abstract:
BACKGROUND:Domains containing the beta-grasp fold are utilized in a great diversity of physiological functions but their role, if any, in soluble or small molecule ligand recognition is poorly studied. RESULTS:Using sensitive sequence and structure similarity searches we identify a novel superfamily containing the beta-grasp fold. They are found in a diverse set of proteins that include the animal vitamin B12 uptake proteins transcobalamin and intrinsic factor, the bacterial polysaccharide export proteins, the competence DNA receptor ComEA, the cob(I)alamin generating enzyme PduS and the Nqo1 subunit of the respiratory electron transport chain. We present evidence that members of this superfamily are likely to bind a range of soluble ligands, including B12. There are two major clades within this superfamily, namely the transcobalamin-like clade and the Nqo1-like clade. The former clade is typified by an insert of a beta-hairpin after the helix of the beta-grasp fold, whereas the latter clade is characterized by an insert between strands 4 and 5 of the core fold. CONCLUSION:Members of both clades within this superfamily are predicted to interact with ligands in a similar spatial location, with their specific inserts playing a role in the process. Both clades are widely represented in bacteria suggesting that this superfamily was derived early in bacterial evolution. The animal lineage appears to have acquired the transcobalamin-like proteins from low GC Gram-positive bacteria, and this might be correlated with the emergence of the ability to utilize B12 produced by gut bacteria. REVIEWERS:This article was reviewed by Andrei Osterman, Igor Zhulin, and Arcady Mushegian.
journal_name
Biol Directjournal_title
Biology directauthors
Burroughs AM,Balaji S,Iyer LM,Aravind Ldoi
10.1186/1745-6150-2-4subject
Has Abstractpub_date
2007-01-24 00:00:00pages
4issn
1745-6150pii
1745-6150-2-4journal_volume
2pub_type
杂志文章相关文献
Biology Direct文献大全abstract:BACKGROUND:The current analysis of transposon elements (TE) in Drosophila melanogaster at Evolution Canyon, (EC), Israel, is based on data and analysis done by our collaborators (Drs. J. Gonzalez, J. Martinez and W. Makalowski, this issue). They estimated the frequencies of 28 TEs (transposon elements) in fruit flies (...
journal_title:Biology direct
pub_type: 杂志文章
doi:10.1186/s13062-015-0074-5
更新日期:2015-10-14 00:00:00
abstract::LINE-1 (L1) retrotransposons are repetitive elements in mammalian genomes. They are capable of synthesizing DNA on their own RNA templates by harnessing reverse transcriptase (RT) that they encode. Abundantly expressed full-length L1s and their RT are found to globally influence gene expression profiles, differentiati...
journal_title:Biology direct
pub_type: 杂志文章,评审
doi:10.1186/1745-6150-8-22
更新日期:2013-09-13 00:00:00
abstract::Shannon entropy is used to provide an estimate of the number of interpretable components in a principal component analysis. In addition, several ad hoc stopping rules for dimension determination are reviewed and a modification of the broken stick model is presented. The modification incorporates a test for the presenc...
journal_title:Biology direct
pub_type: 杂志文章
doi:10.1186/1745-6150-2-2
更新日期:2007-01-17 00:00:00
abstract:BACKGROUND:Phagocytosis, that is, engulfment of large particles by eukaryotic cells, is found in diverse organisms and is often thought to be central to the very origin of the eukaryotic cell, in particular, for the acquisition of bacterial endosymbionts including the ancestor of the mitochondrion. RESULTS:Comparisons...
journal_title:Biology direct
pub_type: 杂志文章
doi:10.1186/1745-6150-4-9
更新日期:2009-02-26 00:00:00
abstract:BACKGROUND:Accurate estimation of the isoelectric point (pI) based on the amino acid sequence is useful for many analytical biochemistry and proteomics techniques such as 2-D polyacrylamide gel electrophoresis, or capillary isoelectric focusing used in combination with high-throughput mass spectrometry. Additionally, p...
journal_title:Biology direct
pub_type: 杂志文章
doi:10.1186/s13062-016-0159-9
更新日期:2016-10-21 00:00:00
abstract::It is well-known that Charles Darwin sketched abstract trees of relationship in his 1837 notebook, and depicted a tree in the Origin of Species (1859). Here I attempt to place Darwin's trees in historical context. By the mid-Eighteenth century the Great Chain of Being was increasingly seen to be an inadequate descript...
journal_title:Biology direct
pub_type: 历史文章,杂志文章,评审
doi:10.1186/1745-6150-4-43
更新日期:2009-11-16 00:00:00
abstract:BACKGROUND:Recent studies suggest that gene expression profiles are a promising alternative for clinical cancer classification. One major problem in applying DNA microarrays for classification is the dimension of obtained data sets. In this paper we propose a multiclass gene selection method based on Partial Least Squa...
journal_title:Biology direct
pub_type: 杂志文章
doi:10.1186/1745-6150-7-33
更新日期:2012-10-02 00:00:00
abstract:BACKGROUND:In eukaryotes, RNA interference (RNAi) is a major mechanism of defense against viruses and transposable elements as well of regulating translation of endogenous mRNAs. The RNAi systems recognize the target RNA molecules via small guide RNAs that are completely or partially complementary to a region of the ta...
journal_title:Biology direct
pub_type: 杂志文章
doi:10.1186/1745-6150-4-29
更新日期:2009-08-25 00:00:00
abstract:BACKGROUND:Synthesis of proteins is based on the genetic code - a nearly universal assignment of codons to amino acids (aas). A major challenge to the understanding of the origins of this assignment is the archetypal "key-lock vs. frozen accident" dilemma. Here we re-examine this dilemma in light of 1) the fundamental ...
journal_title:Biology direct
pub_type: 杂志文章
doi:10.1186/1745-6150-6-14
更新日期:2011-02-22 00:00:00
abstract:BACKGROUND:The elucidation of the dominant role of horizontal gene transfer (HGT) in the evolution of prokaryotes led to a severe crisis of the Tree of Life (TOL) concept and intense debates on this subject. CONCEPT:Prompted by the crisis of the TOL, we attempt to define the primary units and the fundamental patterns ...
journal_title:Biology direct
pub_type: 杂志文章
doi:10.1186/1745-6150-4-33
更新日期:2009-09-29 00:00:00
abstract:BACKGROUND:In the past, many methods have been developed for peptide tertiary structure prediction but they are limited to peptides having natural amino acids. This study describes a method PEPstrMOD, which is an updated version of PEPstr, developed specifically for predicting the structure of peptides containing natur...
journal_title:Biology direct
pub_type: 杂志文章
doi:10.1186/s13062-015-0103-4
更新日期:2015-12-21 00:00:00
abstract:BACKGROUND:A dramatic increase in the prevalence of autism and Autistic Spectrum Disorders (ASD) has been observed over the last two decades in USA, Europe and Asia. Given the accumulating data on the possible role of translation in the etiology of ASD, we analyzed potential effects of rare synonymous substitutions ass...
journal_title:Biology direct
pub_type: 杂志文章
doi:10.1186/1745-6150-9-16
更新日期:2014-07-10 00:00:00
abstract::A widespread and highly conserved family of apparently inactivated derivatives of archaeal B-family DNA polymerases is described. Phylogenetic analysis shows that the inactivated forms comprise a distinct clade among archaeal B-family polymerases and that, within this clade, Euryarchaea and Crenarchaea are clearly sep...
journal_title:Biology direct
pub_type: 杂志文章
doi:10.1186/1745-6150-3-32
更新日期:2008-08-06 00:00:00
abstract:BACKGROUND:The transition from premalignant to invasive tumour growth is a prolonged multistep process governed by phenotypic adaptation to changing microenvironmental selection pressures. Cancer prevention strategies are required to interrupt or delay somatic evolution of the malignant invasive phenotype. Empirical st...
journal_title:Biology direct
pub_type: 杂志文章
doi:10.1186/1745-6150-5-22
更新日期:2010-04-20 00:00:00
abstract:BACKGROUND:The overwhelming majority of animal species exhibit bilateral symmetry. However, the precise evolutionary importance of bilateral symmetry is unknown, although elements of the understanding of the phenomenon have been present within the scientific community for decades. PRESENTATION OF THE HYPOTHESIS:Here w...
journal_title:Biology direct
pub_type: 杂志文章
doi:10.1186/1745-6150-7-22
更新日期:2012-07-12 00:00:00
abstract::Functional biologists, like Claude Bernard, ask "How?", meaning that they investigate the mechanisms underlying the emergence of biological functions (proximal causes), while evolutionary biologists, like Charles Darwin, asks "Why?", meaning that they search the causes of adaptation, survival and evolution (remote cau...
journal_title:Biology direct
pub_type: 杂志文章
doi:10.1186/s13062-016-0109-6
更新日期:2016-02-09 00:00:00
abstract:UNLABELLED:In this work we review past articles that have mathematically studied cancer heterogeneity and the impact of this heterogeneity on the structure of optimal therapy. We look at past works on modeling how heterogeneous tumors respond to radiotherapy, and take a particularly close look at how the optimal radiot...
journal_title:Biology direct
pub_type: 杂志文章,评审
doi:10.1186/s13062-016-0142-5
更新日期:2016-08-23 00:00:00
abstract:UNLABELLED:Pseudogenes arise from the decay of gene copies following either RNA-mediated duplication (processed pseudogenes) or DNA-mediated duplication (nonprocessed pseudogenes). Here, we show that long protein-coding genes tend to produce more nonprocessed pseudogenes than short genes, whereas the opposite is true f...
journal_title:Biology direct
pub_type: 杂志文章
doi:10.1186/1745-6150-4-38
更新日期:2009-10-06 00:00:00
abstract:BACKGROUND:A single cultured marine organism, Nanoarchaeum equitans, represents the Nanoarchaeota branch of symbiotic Archaea, with a highly reduced genome and unusual features such as multiple split genes. RESULTS:The first terrestrial hyperthermophilic member of the Nanoarchaeota was collected from Obsidian Pool, a ...
journal_title:Biology direct
pub_type: 杂志文章
doi:10.1186/1745-6150-8-9
更新日期:2013-04-22 00:00:00
abstract::All modern cells are bounded by cell membranes best described by the fluid mosaic model. This statement is so widely accepted by biologists that little attention is generally given to the theoretical importance of cell membranes in describing the cell. This has not always been the case. When the Cell Theory was first ...
journal_title:Biology direct
pub_type: 历史文章,杂志文章,评审
doi:10.1186/s13062-014-0032-7
更新日期:2014-12-19 00:00:00
abstract:INTRODUCTION:Three major outer membrane protein genes of Escherichia coli, ompF, ompC, and ompA respond to stress factors. Transcripts from these genes are regulated by the small non-coding RNAs micF, micC, and micA, respectively. Here we examine Photorhabdus luminescens, an organism that has a different habitat from E...
journal_title:Biology direct
pub_type: 杂志文章
doi:10.1186/1745-6150-1-12
更新日期:2006-05-22 00:00:00
abstract:BACKGROUND:Long-lived marine megavertebrates (e.g. sharks, turtles, mammals, and seabirds) are inherently vulnerable to anthropogenic mortality. Although some mathematical models have been applied successfully to manage these animals, more detailed treatments are often needed to assess potential drivers of population d...
journal_title:Biology direct
pub_type: 杂志文章
doi:10.1186/1745-6150-9-23
更新日期:2014-11-18 00:00:00
abstract:BACKGROUND:The availability of over 3000 published genome sequences has enabled the use of comparative genomic approaches to drive the biological function discovery process. Classically, one used to link gene with function by genetic or biochemical approaches, a lengthy process that often took years. Phylogenetic distr...
journal_title:Biology direct
pub_type: 杂志文章
doi:10.1186/1745-6150-7-32
更新日期:2012-09-26 00:00:00
abstract:BACKGROUND:The translation machinery underlies a multitude of biological processes within the cell. The design and implementation of the modern translation apparatus on even the simplest course of action is extremely complex, and involves different RNA and protein factors. According to the "RNA world" idea, the critica...
journal_title:Biology direct
pub_type: 杂志文章
doi:10.1186/1745-6150-8-17
更新日期:2013-07-08 00:00:00
abstract::tRNA-derived RNA fragments (tRFs) are 19mer small RNAs that associate with Argonaute (AGO) proteins in humans. However, in plants, it is unknown if tRFs bind with AGO proteins. Here, using public deep sequencing libraries of immunoprecipitated Argonaute proteins (AGO-IP) and bioinformatics approaches, we identified th...
journal_title:Biology direct
pub_type: 杂志文章
doi:10.1186/1745-6150-8-6
更新日期:2013-02-12 00:00:00
abstract:BACKGROUND:The origin of the selective nuclear protein import machinery, which consists of nuclear pore complexes and adaptor molecules interacting with the nuclear localization signals (NLSs) of cargo molecules, is one of the most important events in the evolution of eukaryotic cells. How proteins were selected for im...
journal_title:Biology direct
pub_type: 杂志文章
doi:10.1186/s13062-020-00263-6
更新日期:2020-04-28 00:00:00
abstract:BACKGROUND:Drug-induced liver injury (DILI) is a major concern in drug development, as hepatotoxicity may not be apparent at early stages but can lead to life threatening consequences. The ability to predict DILI from in vitro data would be a crucial advantage. In 2018, the Critical Assessment Massive Data Analysis gro...
journal_title:Biology direct
pub_type: 杂志文章
doi:10.1186/s13062-020-0259-4
更新日期:2020-02-13 00:00:00
abstract:BACKGROUND:While all codons that specify amino acids are universally recognized by tRNA molecules, codons signaling termination of translation are recognized by proteins known as class-I release factors (RF). In most eukaryotes and archaea a single RF accomplishes termination at all three stop codons. In most bacteria,...
journal_title:Biology direct
pub_type: 杂志文章
doi:10.1186/1745-6150-1-28
更新日期:2006-09-13 00:00:00
abstract:BACKGROUND:While the local-mode HMMER3 is notable for its massive speed improvement, the slower glocal-mode HMMER2 is more exact for domain annotation by enforcing full domain-to-sequence alignments. Since a unit of domain necessarily implies a unit of function, local-mode HMMER3 alone remains insufficient for precise ...
journal_title:Biology direct
pub_type: 杂志文章
doi:10.1186/s13062-016-0163-0
更新日期:2016-11-29 00:00:00
abstract:BACKGROUND:Several computational candidate gene selection and prioritization methods have recently been developed. These in silico selection and prioritization techniques are usually based on two central approaches--the examination of similarities to known disease genes and/or the evaluation of functional annotation of...
journal_title:Biology direct
pub_type: 杂志文章
doi:10.1186/1745-6150-6-30
更新日期:2011-06-13 00:00:00