Abstract：
UNLABELLED:Recently Mycobacterium tuberculosis was shown to possess a novel protein modification, in which a small protein Pup is conjugated to the epsilon-amino groups of lysines in target proteins. Analogous to ubiquitin modification in eukaryotes, this remarkable modification recruits proteins for degradation via archaeal-type proteasomes found in mycobacteria and allied actinobacteria. While a mycobacterial protein named PafA was found to be required for this conjugation reaction, its biochemical mechanism has not been elucidated. Using sensitive sequence profile comparison methods we establish that the PafA family proteins are related to the gamma-glutamyl-cysteine synthetase and glutamine synthetase. Hence, we predict that PafA is the Pup ligase, which catalyzes the ATP-dependent ligation of the terminal gamma-carboxylate of glutamate to lysines, similar to the above enzymes. We further discovered that an ortholog of the eukaryotic PAC2 (e.g. cg2106) is often present in the vicinity of the actinobacterial Pup-proteasome gene neighborhoods and is likely to represent the ancestral proteasomal chaperone. Pup-conjugation is sporadically present outside the actinobacteria in certain lineages, such as verrucomicrobia, nitrospirae, deltaproteobacteria and planctomycetes, and in the latter two lineages it might modify membrane proteins. REVIEWERS:This article was reviewed by M. Madan Babu and Andrei Osterman.
journal_name
Biol Directjournal_title
Biology directauthors
Iyer LM,Burroughs AM,Aravind Ldoi
10.1186/1745-6150-3-45subject
Has Abstractpub_date
2008-11-03 00:00:00pages
45issn
1745-6150pii
1745-6150-3-45journal_volume
3pub_type
杂志文章相关文献
Biology Direct文献大全abstract：UNLABELLED:Primase and GINS are essential factors for chromosomal DNA replication in eukaryotic and archaeal cells. Here we describe a previously undetected relationship between the C-terminal domain of the catalytic subunit (PriS) of archaeal primase and the B-domains of the archaeo-eukaryotic GINS proteins in the for...
journal_title：Biology direct
pub_type： 杂志文章
doi：10.1186/1745-6150-5-17
更新日期：2010-04-12 00:00:00
abstract：BACKGROUND:The advent of metagenomic sequencing provides microbial abundance patterns that can be leveraged for sample origin prediction. Supervised machine learning classification approaches have been reported to predict sample origin accurately when the origin has been previously sampled. Using metagenomic datasets p...
journal_title：Biology direct
pub_type： 杂志文章
doi：10.1186/s13062-020-00287-y
更新日期：2020-12-10 00:00:00
abstract：BACKGROUND:Microbial communities play a crucial role in our environment and may influence human health tremendously. Despite being the place where human interaction is most abundant we still know little about the urban microbiome. This is highlighted by the large amount of unclassified DNA reads found in urban metageno...
journal_title：Biology direct
pub_type： 杂志文章
doi：10.1186/s13062-018-0225-6
更新日期：2018-10-12 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：: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：:The concept of developmental constraints has been central to understand the role of development in morphological evolution. Developmental constraints are classically defined as biases imposed by development on the distribution of morphological variation.This opinion article argues that the concepts of developmental co...
journal_title：Biology direct
pub_type： 杂志文章
doi：10.1186/s13062-020-00289-w
更新日期：2021-01-09 00:00:00
abstract：BACKGROUND:An evolutionary classification of genes from sequenced genomes that distinguishes between orthologs and paralogs is indispensable for genome annotation and evolutionary reconstruction. Shortly after multiple genome sequences of bacteria, archaea, and unicellular eukaryotes became available, an attempt on suc...
journal_title：Biology direct
pub_type： 杂志文章
doi：10.1186/1745-6150-2-33
更新日期：2007-11-27 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：: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：:Plant viruses of the recently recognized family Amalgaviridae have monopartite double-stranded (ds) RNA genomes and encode two proteins: an RNA-dependent RNA polymerase (RdRp) and a putative capsid protein (CP). Whereas the RdRp of amalgaviruses has been found to be most closely related to the RdRps of dsRNA viruses o...
journal_title：Biology direct
pub_type： 杂志文章
doi：10.1186/s13062-015-0047-8
更新日期：2015-03-29 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: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:In the presence of horizontal gene transfer (HGT), the concepts of lineage and genealogy in the microbial world become more ambiguous because chimeric genomes trace their ancestry from a myriad of sources, both living and extinct. RESULTS:We present the evolutionary histories of three aminoacyl-tRNA synthet...
journal_title：Biology direct
pub_type： 杂志文章
doi：10.1186/1745-6150-6-47
更新日期：2011-09-23 00:00:00
abstract：BACKGROUND:Currently a huge amount of protein-protein interaction data is available therefore extracting meaningful ones are a challenging task. In a protein-protein interaction network, hubs are considered as key proteins maintaining function and stability of the network. Therefore, studying protein-protein complexes ...
journal_title：Biology direct
pub_type： 杂志文章
doi：10.1186/1745-6150-6-49
更新日期：2011-10-05 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：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:Many studies of biochemical networks have analyzed network topology. Such work has suggested that specific types of network wiring may increase network robustness and therefore confer a selective advantage. However, knowledge of network topology does not allow one to predict network dynamical behavior--for e...
journal_title：Biology direct
pub_type： 杂志文章
doi：10.1186/1745-6150-3-49
更新日期：2008-12-04 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：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: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: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 bet...
journal_title：Biology direct
pub_type： 杂志文章
doi：10.1186/1745-6150-2-4
更新日期：2007-01-24 00:00:00
abstract：BACKGROUND:The rice blast disease caused by Magnaporthe oryzae is a major constraint on world rice production. The conidia produced by this fungal pathogen are the main source of disease dissemination. The morphology of conidia may be a critical factor in the spore dispersal and virulence of M. oryzae in the field. Del...
journal_title：Biology direct
pub_type： 杂志文章
doi：10.1186/1745-6150-5-61
更新日期：2010-11-02 00:00:00
abstract：BACKGROUND:The prokaryotic toxin-antitoxin systems (TAS, also referred to as TA loci) are widespread, mobile two-gene modules that can be viewed as selfish genetic elements because they evolved mechanisms to become addictive for replicons and cells in which they reside, but also possess "normal" cellular functions in v...
journal_title：Biology direct
pub_type： 杂志文章
doi：10.1186/1745-6150-4-19
更新日期：2009-06-03 00:00:00
abstract：BACKGROUND:It is common belief that all cellular life forms on earth have a common origin. This view is supported by the universality of the genetic code and the universal conservation of multiple genes, particularly those that encode key components of the translation system. A remarkable recent study claims to provide...
journal_title：Biology direct
pub_type： 杂志文章
doi：10.1186/1745-6150-5-64
更新日期：2010-11-18 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: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：: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：:Two apparently irreconcilable models dominate research into the origin of eukaryotes. In one model, amitochondrial proto-eukaryotes emerged autogenously from the last universal common ancestor of all cells. Proto-eukaryotes subsequently acquired mitochondrial progenitors by the phagocytic capture of bacteria. In the s...
journal_title：Biology direct
pub_type： 杂志文章
doi：10.1186/s13062-020-00260-9
更新日期：2020-04-28 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 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
