Nomenclature For Proteins Research Articles

Characterisation and expression of a novel haplotype cry2A-type gene from Bacillus thuringiensis strain JF19-2

The Bacillus thuringiensis isolate JF19-2, a native organism found in soil samples from the Sichuan Basin in western China, contains a bipyramidal crystal harbouring one insecticidal crystal protein (about 70 kDa). Interestingly, a novel cry2A-type gene, encoding a 635 amino acid protein with 92% homology to cry2Ab1, was found and cloned from this strain. According to the nomenclature principles adopted for B. thuringiensis insecticidal crystal proteins, this gene represents a novel haplotype cry gene and was designated as cry2Ag1 by the Bacillus thuringiensis Pesticide Crystal Protein Nomenclature Committee. Cry2Ag1 was expressed in Escherichia coli BL21(DE3)pLysS cells, and the results of insecticidal activity assays showed that Cry2Ag1 was toxic to both Dipteran (Aedes aegypti) and Lepidopteran (Plutella xylostella and Helicoverpa armigera) pests. These results strongly suggest that the cloning of the cry2Ag1 gene is not only of interest to researchers studying insecticidal crystal genes, but may ultimately serve as a solution to the increasing resistance of pests to currently used insecticides.

ATF3, a Hub of the Cellular Adaptive-Response Network, in the Pathogenesis of Diseases: Is Modulation of Inflammation a Unifying Component?

Activating transcription factor 3 (ATF3) gene encodes a member of the ATF family of transcription factors and is induced by various stress signals. All members of this family share the basic region-leucine zipper (bZip) DNA binding motif and bind to the consensus sequence TGACGTCA in vitro. Previous reviews and an Internet source have covered the following topics: the nomenclature of ATF proteins, the history of their discovery, the potential interplays between ATFs and other bZip proteins, ATF3-interacting proteins, ATF3 target genes, and the emerging roles of ATF3 in cancer and immunity (see footnote 1). In this review, we present evidence and clues that prompted us to put forth the idea that ATF3 functions as a "hub" of the cellular adaptive-response network. We will then focus on the roles of ATF3 in modulating inflammatory response. Inflammation is increasingly recognized to play an important role for the development of many diseases. Putting this in the context of the hub idea, we propose that modulation of inflammation by ATF3 is a unifying theme for the potential involvement of ATF3 in various diseases.

Emerging issues with the current keratin-associated protein nomenclature

Keratin associated proteins (KAPs) are a class of proteins that associate with keratin intermediate filament proteins through disulphide linkages to give fibres such as hair and wool their unique properties. Up to 90 proteins from some 25 families have been identified and this does not include polymorphic variants of individual proteins within these families. The existence of this diverse group of proteins has been known for some 75 years but, despite this, there is still no universally accepted nomenclature for them. This paper sets out the case for revising the current system to deal with this nomenclature issue.

The Protein Naming Utility: a rules database for protein nomenclature

Generation of syntactically correct and unambiguous names for proteins is a challenging, yet vital task for functional annotation processes. Proteins are often named based on homology to known proteins, many of which have problematic names. To address the need to generate high-quality protein names, and capture our significant experience correcting protein names manually, we have developed the Protein Naming Utility (PNU, http://www.jcvi.org/pn-utility). The PNU is a web-based database for storing and applying naming rules to identify and correct syntactically incorrect protein names, or to replace synonyms with their preferred name. The PNU allows users to generate and manage collections of naming rules, optionally building upon the growing body of rules generated at the J. Craig Venter Institute (JCVI). Since communities often enforce disparate conventions for naming proteins, the PNU supports grouping rules into user-managed collections. Users can check their protein names against a selected PNU rule collection, generating both statistics and corrected names. The PNU can also be used to correct GenBank table files prior to submission to GenBank. Currently, the database features 3080 manual rules that have been entered by JCVI Bioinformatics Analysts as well as 7458 automatically imported names.

Cyclin-dependent kinases: a family portrait

To the Editor, Cyclin-dependent kinases (CDKs) are protein kinases involved in critical cellular processes, such as cell cycle or transcription, whose activity requires association with specific cyclin subunits. Based on sequence similarity, the human genome contains 21 genes encoding CDKs and five additional genes encoding a more distant group of proteins known as CDK-like (CDKL) kinases. The current nomenclature for CDK proteins includes 11 classical CDKs (CDK1–11), two newly proposed family members (CDK12 and 13) and additional proteins whose names are based on the presence of a cyclin-binding element (PFTAIRE and PCTAIRE proteins) or simply based on a sequence relationship with the original CDKs, such as CDC2-like kinases (CDC2L) or cell cycle-related kinases (CCRK)

Characterization of insecticidal crystal proteincry gene ofBacillus thuringiensis from soil of Sichuan Basin, China and cloning of novel haplotypescry gene

In order to systematically investigate the cry gene resources from Bacillus thuringiensis (Bt) in different ecological regions in Sichuan Basin and further clone novel cry genes. We used the methods of microscopic and scanning electron microscopic observation, PCR-restriction fragment length polymorphism (PCR-RFLP) analysis, sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), and test of insecticidal activities to research Bt strains collected in this basin. We screened 791 Bt isolates from 2650 soil samples, and found cryl, cry2, cry3, cry4/10, cry9, cry30, and cry40-type genes in this basin. Strains containing cryl genes were the most abundant in our collection (66%), and 21 different cry1-type gene combinations were found. Furthermore, several novel holotype cry genes were found and the full-length sequences of 3 novel cry genes were designated as cry54Aa1, cry30Fa1, and cry30 Ga1 by B. thuringiensis Pesticidal Crystal Protein Nomenclature Committee. The results of insecticidal activities showed that Sichuan Basin harbored Bt isolates with insecticidal activities. SDS-PAGE assay of 80 strains without PCR products indicated that these strains may harbor potentially novel cry proteins gene. The diversity and particularity of cry gene resources in Sichuan Basin have important meanings in theories and practices.

Cloning, expression and activity ofcry1Iagene fromBacillus thuringiensisisolate

AbstractA full-lengthcry1Iagene fragment, obtained by polymerase chain reaction (PCR) amplification with a pair of primers designed according tocry1Ia-type gene sequences and DNA fromBacillus thuringiensisas template, was introduced into the expression vector pET-21b and transformed intoEscherichia coliBL21(DE3). The molecular weight of the induced expression product was 81.2 kDa. The amino acid sequence of Cry1Ia was very different from sequences of 12 known Cry1Ia-type proteins. This gene was designated ascry1Ia8by the InternationalB. thuringiensisInsecticidal Protein Nomenclature Committee (accession number AF373207). The bioassay results indicated that Cry1Ia toxin protein showed distinct insecticidal activity againstOstrinia furnacalisandPlutella xylostellawith LC50of 0.268 μg/g and 2.227 μg/ml, respectively. It also had insecticidal activity againstLeguminivora glycinivorella, but not againstPyrrhalta aenescens. The novelcry1Ia8gene will be an important resource in constructing genetically engineered bacteria and transgenic plants for biocontrol of insect pests. It is also available for screening gene stacks to delay pest resistance.

Functional Analysis of Picornavirus 2B Proteins: Effects on Calcium Homeostasis and Intracellular Protein Trafficking

The family Picornaviridae consists of a large group of plus-strand RNA viruses that share a similar genome organization. The nomenclature of the picornavirus proteins is based on their position in the viral RNA genome but does not necessarily imply a conserved function of proteins of different genera. The enterovirus 2B protein is a small hydrophobic protein that, upon individual expression, is localized to the endoplasmic reticulum (ER) and the Golgi complex, reduces ER and Golgi complex Ca(2+) levels, most likely by forming transmembrane pores, and inhibits protein trafficking through the Golgi complex. At present, little is known about the function of the other picornavirus 2B proteins. Here we show that rhinovirus 2B, which is phylogenetically closely related to enterovirus 2B, shows a similar subcellular localization and function to those of enterovirus 2B. In contrast, 2B proteins of hepatitis A virus, foot-and-mouth disease virus, and encephalomyocarditis virus, all of which are more distantly related to enteroviruses, show a different localization and have little, if any, effects on Ca(2+) homeostasis and intracellular protein trafficking. Our data suggest that the 2B proteins of enterovirus and rhinovirus share the same function in virus replication, while the other picornavirus 2B proteins support the viral life cycle in a different manner. Moreover, we show that an enterovirus 2B protein that is retained in the ER is unable to modify Ca(2+) homeostasis and inhibit protein trafficking, demonstrating the importance of Golgi complex localization for its functioning.

DYRK1A-mediated Hyperphosphorylation of Tau

Most individuals with Down syndrome show early onset of Alzheimer disease (AD), resulting from the extra copy of chromosome 21. Located on this chromosome is a gene that encodes the dual specificity tyrosine phosphorylation-regulated kinase 1A (DYRK1A). One of the pathological hallmarks in AD is the presence of neurofibrillary tangles (NFTs), which are insoluble deposits that consist of abnormally hyperphosphorylated Tau. Previously it was reported that Tau at the Thr-212 residue was phosphorylated by Dyrk1A in vitro. To determine the physiological significance of this phosphorylation, an analysis was made of the amount of phospho-Thr-212-Tau (pT212) in the brains of transgenic mice that overexpress the human DYRK1A protein (DYRK1A TG mice) that we recently generated. A significant increase in the amount of pT212 was found in the brains of DYRK1A transgenic mice when compared with age-matched littermate controls. We further examined whether Dyrk1A phosphorylates other Tau residues that are implicated in NFTs. We found that Dyrk1A also phosphorylates Tau at Ser-202 and Ser-404 in vitro. Phosphorylation by Dyrk1A strongly inhibited the ability of Tau to promote microtubule assembly. Following this, using mammalian cells and DYRK1A TG mouse brains, it was demonstrated that the amounts of phospho-Ser-202-Tau and phospho-Ser-404-Tau are enhanced when DYRK1A amounts are high. These results provide the first in vivo evidence for a physiological role of DYRK1A in the hyperphosphorylation of Tau and suggest that the extra copy of the DYRK1A gene contributes to the early onset of AD.

Analysis of 22 mutations within milk protein genes in Italian Friesian cattle

xsThe bovine milk protein caseins, αS1-CN, β-CN, αS2-CN, and κ-CN are codified by four well characterized genes, named CSN1S1, CSN2, CSN1S2, and CSN3 respectively and clustered in a region of 250-kb of chromosome 6. A recent revision of milk protein nomenclature considering only protein polymorphisms indicates 8 αS1-CN, 4 αS2-CN, 12 β-CN, and 11 κ-CN variants within the genus Bos. Other mutations were found in the non-coding regions of the cluster, such as the promoter regions or the 3’UTR.Many of these polymorphisms, together with others in various genes, such as the one coding for β-lactoglobulin (LGB), show important associations with different milk quality traits. Analyzing all these polymorphisms could help clarify the role of both the casein haplotype and the other polymorphisms in milk composition and cheese-making properties, and could explain which polymorphisms are really or mostly involved. The mPCR-LDR-UA approach recently developed to test simultaneously 22 SNPs in DNA regions responsible for milk protein expression was used to type 250 Italian Friesian cattle. In perfect agreement with literature, the most frequent alleles were CSN1S1*B, CSN2*A2, CSN3*A, variant 2 of CSN1S1 promoter, and variant A of Bov-A2 element.A quite balanced frequency was observed for the LGB*A and LGB*B. No CSN2*C, CSN3*C, and CSN3*H alleles were found. The CSN1S1*C, CSN2*A3, CSN2*I alleles were detected only at the heterozygous condition and at a frequency lower than 2%. The method allowed also finding some unusual intragenic haplotype, such as the Bov-A2 element-CSN3 haplotypes A-B and B-E. As to LGB one of the four SNPs tested was always homozygous for the same mutation, as already noticed.This finding confirms that this synonymous SNP is probably a sequencing mistake or a rare mutation not decisive for the LGB typing in the Italian Friesian. Reducing cost and time for typing simultaneously many SNPs, the method will be applied to a greater number of individuals and to other breeds, aiming to find out a number of animals for each haplotype sufficient for accurate statistical analysis to give a better understanding of the significance of milk protein polymorphism.

Strategy for amplification and sequencing of insecticidal cry1A genes from Bacillus thuringiensis

A feasible and fully described strategy, with a detailed list of primers, for amplifying, cloning and sequencing known and potentially novel cry1A genes harboured by a Bacillus thuringiensis strain was successfully established. Based on the analysis of conserved regions of the cry1A genes, the 1AF and 1UR oligonucleotide primers were designed to amplify the whole open reading frame of these genes. The PCR products obtained revealed the successful amplification of cry1A genes from 13 B. thuringiensis strains. These bacteria were previously known to harbour at least one cry1A gene. An Argentinean B. thuringiensis isolate INTA Mo1-12 was randomly chosen for cloning and sequencing of cry1A genes by using a primer set developed in this study. Both nucleotide and amino acid sequences similarity analysis revealed that cry1Aa and cry1Ac from B. thuringiensis INTA Mo1-12 are new natural variants, showing several differences with the other known cry1A subclasses. These genes were named by the B. thuringiensis Pesticidal Crystal Protein Nomenclature Committee as cry1Aa15 and cry1Ac21 respectively.

The Aminoterminal Insulin-Like Growth Factor (IGF) Binding Domain of IGF Binding Protein-3 Cannot Be Functionally Substituted by the Structurally Homologous Domain of CCN3

IGF binding proteins (IGFBPs) are a family of structurally homologous proteins that bind IGFs with high affinities and can modulate IGF activity. The IGF binding site has been shown to comprise residues in both the aminoterminal and carboxyterminal domains. In recent years several proteins including members of the CCN (connective tissue growth factor, Cyr61, and nephroblastoma overexpressed) family were recognized as having structural homology in their aminoterminal domains to the IGFBPs. Despite their low or undetectable IGF binding ability, a proposal was made to rename them as IGFBP-related proteins. To test whether the aminoterminal domain of a CCN protein can fulfill the high-affinity IGF binding function of an IGFBP, we created a chimera in which the aminoterminal domain of IGFBP-3 was substituted with the aminoterminal domain of CCN3 (previously known as Nov). The CCN3-IGFBP-3 chimera bound IGFs and inhibited IGF activity very weakly, similar to CCN3 itself. Although structurally similar, the aminoterminal domain of CCN3 is unable to replace the aminoterminal domain of IGFBP-3 in forming a high-affinity IGF-binding site. These results argue against a direct role of CCN3 in the regulation of IGF bioavailability and indicate that the nomenclature of IGFBP-related proteins (which implies functional relationship to the classical IGFBPs) is inappropriate for CCN proteins.

Gene and protein nomenclature in public databases.

BackgroundFrequently, several alternative names are in use for biological objects such as genes and proteins. Applications like manual literature search, automated text-mining, named entity identification, gene/protein annotation, and linking of knowledge from different information sources require the knowledge of all used names referring to a given gene or protein. Various organism-specific or general public databases aim at organizing knowledge about genes and proteins. These databases can be used for deriving gene and protein name dictionaries. So far, little is known about the differences between databases in terms of size, ambiguities and overlap.ResultsWe compiled five gene and protein name dictionaries for each of the five model organisms (yeast, fly, mouse, rat, and human) from different organism-specific and general public databases. We analyzed the degree of ambiguity of gene and protein names within and between dictionaries, to a lexicon of common English words and domain-related non-gene terms, and we compared different data sources in terms of size of extracted dictionaries and overlap of synonyms between those.The study shows that the number of genes/proteins and synonyms covered in individual databases varies significantly for a given organism, and that the degree of ambiguity of synonyms varies significantly between different organisms. Furthermore, it shows that, despite considerable efforts of co-curation, the overlap of synonyms in different data sources is rather moderate and that the degree of ambiguity of gene names with common English words and domain-related non-gene terms varies depending on the considered organism.ConclusionIn conclusion, these results indicate that the combination of data contained in different databases allows the generation of gene and protein name dictionaries that contain significantly more used names than dictionaries obtained from individual data sources. Furthermore, curation of combined dictionaries considerably increases size and decreases ambiguity.The entries of the curated synonym dictionary are available for manual querying, editing, and PubMed- or Google-search via the ProThesaurus-wiki. For automated querying via custom software, we offer a web service and an exemplary client application.

New consensus nomenclature for mammalian keratins

Keratins are intermediate filament–forming proteins that provide mechanical support and fulfill a variety of additional functions in epithelial cells. In 1982, a nomenclature was devised to name the keratin proteins that were known at that point. The systematic sequencing of the human genome in recent years uncovered the existence of several novel keratin genes and their encoded proteins. Their naming could not be adequately handled in the context of the original system. We propose a new consensus nomenclature for keratin genes and proteins that relies upon and extends the 1982 system and adheres to the guidelines issued by the Human and Mouse Genome Nomenclature Committees. This revised nomenclature accommodates functional genes and pseudogenes, and although designed specifically for the full complement of human keratins, it offers the flexibility needed to incorporate additional keratins from other mammalian species.

Down‐regulation of the strawberry Bet v 1‐homologous allergen in concert with the flavonoid biosynthesis pathway in colorless strawberry mutant

Proteomic screening of strawberry (Fragaria ananassa) yielded a 58% success rate in protein identification in spite of the fact that no genomic sequence is available for this species. This was achieved by a combination of MALDI-MS/MS de novo sequencing of double-derivatized peptides and indel-tolerant searching against local protein databases built on both EST and full-length nucleotide sequences. The amino acid sequence of a strawberry allergen, homologous to the well-known major birch pollen allergen Bet v 1, was partially determined. This strawberry allergen, named Fra a 1 according to the nomenclature for allergen proteins, showed sequence identity of 54 and 77%, respectively, with corresponding allergens from birch and apple. Differential expression, as evaluated by 2-D DIGE, occurred in 10% of protein spots when red strawberries were compared to a colorless (white) strawberry mutant. White strawberries, known to be tolerated by individuals affected by allergy, were found to be virtually free from the strawberry allergen. Also several enzymes in the pathway for biosynthesis of flavonoids, to which the red color pelargonidin belongs, were down-regulated. This approach to assess differential protein expression without access to genomic sequence information can also be applied to other crop plants and phenotypic traits.

Proposed revisions to the nomenclature for Brachyspira membrane proteins and lipoproteins

Proposed revisions to the nomenclature for Brachyspira membrane proteins and lipoproteins

DPVweb: a comprehensive database of plant and fungal virus genes and genomes

DPVweb () provides a central source of information about viruses, viroids and satellites of plants, fungi and protozoa. Comprehensive taxonomic information, including brief descriptions of each family and genus, and classified lists of virus sequences are provided. The database also holds detailed, curated, information for all sequences of viruses, viroids and satellites of plants, fungi and protozoa that are complete or that contain at least one complete gene (currently, n ≈ 9000). For comparative purposes, it also contains a single representative sequence of all other fully sequenced virus species with an RNA or single-stranded DNA genome. The start and end positions of each feature (gene, non-translated region and the like) have been recorded and checked for accuracy. As far as possible, nomenclature for genes and proteins are standardized within genera and families. Sequences of features (either as DNA or amino acid sequences) can be directly downloaded from the website in FASTA format. The sequence information can also be accessed via client software for PC computers (freely downloadable from the website) that enable users to make an easy selection of sequences and features of a chosen virus for further analyses.

Tet Protein Hybrids

In their recent letter to the editor (1), Drs. Stanton, Humphrey, Scott, and Flint raised an important point in regard to naming tetracycline resistance determinants in view of the discovery of naturally occurring interclass hybrid proteins. In addition to the current definition of a new gene, i.e., less than 80% amino acid identity to another known tetracycline resistance determinant, we endorse their suggested nomenclature for hybrid determinants and proteins, e.g., Tet O/W (hybrid of Tet O and Tet W) and Tet W/O/W (hybrid of Tet O and Tet W, which has partial Tet O sequence between Tet W ends). The finding of hybrid Tet proteins makes it important, therefore, to sequence entire tet genes to identify such hybrids. The question arises as to how many amino acids corresponding to a second class will define a hybrid. Looking at their data, we suggest that 50 amino acid residues in a single stretch could be appropriate.

A simplified laminin nomenclature

A simplification of the laminin nomenclature is presented. Laminins are multidomain heterotrimers composed of alpha, beta and gamma chains. Previously, laminin trimers were numbered with Arabic numerals in the order discovered, that is laminins-1 to -5. We introduce a new identification system for a trimer using three Arabic numerals, based on the alpha, beta and gamma chain numbers. For example, the laminin with the chain composition alpha5beta1gamma1 is termed laminin-511, and not laminin-10. The current practice is also to mix two overlapping domain and module nomenclatures. Instead of the older Roman numeral nomenclature and mixed nomenclature, all modules are now called domains. Some domains are renamed or renumbered. Laminin epidermal growth factor-like (LE) domains are renumbered starting at the N-termini, to be consistent with general protein nomenclature. Domain IVb of alpha chains is named laminin 4a (L4a), domain IVa of alpha chains is named L4b, domain IV of gamma chains is named L4, and domain IV of beta chains is named laminin four (LF). The two coiled-coil domains I and II are now considered one laminin coiled-coil domain (LCC). The interruption in the coiled-coil of beta chains is named laminin beta-knob (Lbeta) domain. The chain origin of a domain is specified by the chain nomenclature, such as alpha1L4a. The abbreviation LM is suggested for laminin. Otherwise, the nomenclature remains unaltered.

Neurofilament phosphoforms: Surrogate markers for axonal injury, degeneration and loss

This review on the role of neurofilaments as surrogate markers for axonal degeneration in neurological diseases provides a brief background to protein synthesis, assembly, function and degeneration. Methodological techniques for quantification are described and a protein nomenclature is proposed. The relevance for recognising antineurofilament autoantibodies is noted. Pathological implications are discussed in view of immunocytochemical, cell-culture and genetic findings. With reference to the present symposium on multiple sclerosis, the current literature on body fluid levels of neurofilaments in demyelinating disease is summarised.