Evolutionary origins and interactomes of human,young microproteins and small peptides translated from short open reading frames

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Simultaneous high-throughput recombinational cloning of open reading frames in closed and open configurations

Comprehensive open reading frame (ORF) clone collections, ORFeomes, are key components of functional genomics projects. When recombinational cloning systems are used to capture ORFs in master clones, these DNA sequences can be easily transferred into a variety of expression plasmids, each designed for a specific assay. Depending on downstream applications, an ORF is cloned either with or without a stop codon at its original position, referred to as closed or open configuration, respectively. The former is preferred when the encoded protein is produced in its native form or with an amino-terminal tag; the latter is obligatory when the protein is produced as a fusion with a carboxyl-terminal tag. We developed a streamlined protocol for high-throughput, simultaneous cloning of both open and closed ORF entry clones with the Gateway recombinational cloning system. The protocol is straightforward to set up in large-scale ORF cloning projects, and is cost-effective, because the initial ORF amplification and the cloning in a pDONR vector are performed only once to obtain the two ORF configurations. We illustrated its implementation for the isolation and validation of 346 Arabidopsis ORF entry clones.     

人类珠蛋白相关基因上游开放阅读框的变异分析

β-地中海贫血症是一种珠蛋白生成障碍的常染色体隐性遗传病。而γ珠蛋白基因的开放表达和胎儿血红蛋白的合成,是缓解β地中海贫血病人临床表型的一个重要因素。本研究针对202个血红蛋白相关调控基因或miRNA,对1802个β-地中海贫血症患者进行了目标区域捕获测序。通过生物信息学的分析,检测出了所有捕获区域内的突变。进一步对位于5′端非编码区(5′untranslated region, 5′UTR)的突变进行系统扫描,共计寻找到41个影响uORF(upstream open reading frame, uORF)有或无的功能性突变。从中选取了CHTOP基因(chr1:153606541 C>T)和TGFB1基因(chr19:41859418 G>A)的两个突变,通过定点诱变和双荧光素酶报告实验,在体外证实这两个突变均可显著地改变下游基因的表达。该研究结果为β-地中海贫血症临床表型的精确诊断提供了潜在的筛查靶点。     

Expression of antibodies using single open reading frame (sORF) vector design

Efficient production of large quantities of therapeutic antibodies is becoming a major goal of the pharmaceutical industry. We developed a proprietary expression system using a polyprotein precursor-based approach to antibody expression in mammalian cells. In this approach, the coding regions for heavy and light chains are included within a single open reading frame (sORF) separated by an in-frame intein gene. A single mRNA and subsequent polypeptide are produced upon transient and stable transfection into HEK293 and CHO cells, respectively. Heavy and light chains are separated by the autocatalytic action of the intein and antibody processing proceeds to produce active, secreted antibody. Here, we report advances in sORF technology toward establishment of a viable manufacturing platform for therapeutic antibodies in CHO cells. Increasing expression levels and improving antibody processing by intein and signal peptide selection are discussed.     

On the origin of coding sequences from random open reading frames

Summary The size distribution of 411 randomly selected mammalian exons was investigated. This distribution was found to be unimodal with a frequency maximum of 120 bp. Detailed analysis of the distribution demonstrated that larger exons (>150 bp) have a high goodness of fit to the size distribution of open reading frames (ORFs) in a random sequence, i.e., (61/64)^t in which t is the number of triplets. Based on this observation, the general character of the total exon size distribution suggested that this could be defined by a theoretical distribution by superimposing a sigmoid function on the ORF generating function, i.e., (61/64)^t×f_s(t)×E in which f_s(t) is a sigmoid function and E is a constant. We tested this distribution for fitness to the exon distribution using two sigmoid functions. f_s(t)=(t) and f_s(t)=Be^kt/1+Be^kt. In both cases a very high goodness of fit was attained. It is concluded that exons have been generated from ORFs in random sequences, that ORFs larger than 150 bp have been selected, irrespective of size, as exons, and that a lower size limit exists below which the probability of an ORF being selected as an exon is very low. These results provide evidence at the molecular level to support the ideas that (1) larger exons have been selected from random ORFs without primary correlation to structural or functional properties at the protein level, (2) there exists a restriction on smaller ORFs to be selected as exons, and (3) the interrupted coding sequences found in eukaryotes represent the ancient form of gene organization that existed prior to the divergence of prokaryotes and eukaryotes.     

Expression of antibodies using single‐open reading frame vector design and polyprotein processing from mammalian cells

We describe a novel polyprotein precursor‐based approach to express antibodies from mammalian cells. Rather than expressing heavy and light chain proteins from separate expression units, the antibody heavy and light chains are contained in one single‐open reading frame (sORF) separated by an intein gene fused in frame. Inside mammalian cells this ORF is transcribed into a single mRNA, and translated into one polypeptide. The antibody heavy and light chains are separated posttranslationally, assembled into the functional antibody molecule, and secreted into culture medium. It is demonstrated that Pol I intein from P. horikoshii mediates protein splicing and cleavage reactions in mammalian cells, in the context of antibody heavy and light chain amino acid sequences. To allow the separation of antibody heavy chain, light chain, and the intein, we investigated a number of intein mutations designed to inhibit intein‐mediated splicing but preserve cleavage reactions. We have also designed constructs in which the signal peptide downstream from intein has altered hydrophobicity. The use of some of these mutant constructs resulted in more efficient antibody secretion, highlighting areas that can be further explored in improving such an expression system. An antibody secreted using one of the sORF constructs was characterized. This antibody has correct N‐terminal sequences for both of its heavy and light chains, correct heavy and light chain MW as well as intact MW as measured by mass spectrometry. Its affinity to antigen, as measured by surface plasmon resonance (SPR), is indistinguishable from that of the same antibody produced using conventional method. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2009     

Extensive characterization of peptides from Panax ginseng C. A. Meyer using mass spectrometric approach

Panax ginseng is an important herb that has clear effects on the treatment of diverse diseases. Until now, the natural peptide constitution of this herb remains unclear. Here, we conduct an extensive characterization of Ginseng peptidome using MS‐based data mining and sequencing. The screen on the charge states of precursor ions indicated that Ginseng is a peptide‐rich herb in comparison of a number of commonly used herbs. The Ginseng peptides were then extracted and submitted to nano‐LC‐MS/MS analysis using different fragmentation modes, including CID, high‐energy collisional dissociation, and electron transfer dissociation. Further database search and de novo sequencing allowed the identification of total 308 peptides, some of which might have important biological activities. This study illustrates the abundance and sequences of endogenous Ginseng peptides, thus providing the information of more candidates for the screening of active compounds for future biological research and drug discovery studies.     

Rational genomics I: antisense open reading frames and codon bias in short-chain oxido reductase enzymes and the evolution of the genetic code

The short-chain oxidoreductase (SCOR) family of enzymes includes over 6000 members, extending from bacteria and archaea to humans. Nucleic acid sequence analysis reveals that significant numbers of these genes are remarkably free of stopcodons in reading frames other than the coding frame, including those on the antisense strand. The genes from this subset also use almost entirely the GC-rich half of the 64 codons. Analysis of a million hypothetical genes having random nucleotide composition shows that the percentage of SCOR genes having multiple open reading frames exceeds random by a factor of as much as 1 x 10(6). Nevertheless, screening the content of the SWISS-PROT TrEMBL database reveals that 15% of all genes contain multiple open reading frames. The SCOR genes having multiple open reading frames and a GC-rich coding bias exhibit a similar GC bias in the nucleotide triple composition of their DNA. This bias is not correlated with the GC content of the species in which the SCOR genes are found. One possible explanation for the conservation of multiple open reading frames and extreme bias in nucleic acid composition in the family of Rossman folds is that the primordial member of this family was encoded early using only very stable GC-rich DNA and that evolution proceeded with extremely limited introduction of any codons having two or more adenine or thymine nucleotides. These and other data suggest that the SCOR family of enzymes may even have diverged from a common ancestor before most of the AT-rich half of the genetic code was fully defined.     

Antimicrobial activity of short arginine- and tryptophan-rich peptides.

Highly antimicrobial active arginine- and tryptophan-rich peptides were synthesized ranging in size from 11 to five amino acid residues in order to elucidate the main structural requirement for such short antimicrobial peptides. The amino acid sequences of the peptides were based on previous studies of longer bovine and murine lactoferricin derivatives. Most of the peptides showed strong inhibitory action against the Gram-negative bacteria Escherichia coli and Pseudomonas aeruginosa, and the Gram-positive bacterium Staphylococcus aureus. For the most active derivatives, the minimal inhibitory concentration values observed for the Gram-negative bacteria were 5 microg/ml (3.5 microM), whereas it was 2.5 microg/ml (1.5 microM) for the Gram-positive bacterium. It was essential for the antimicrobial activity that the peptides contained a minimum of three tryptophan and three arginine residues, and carried a free N-terminal amino group and an amidated C-terminal end. Furthermore, a minimum sequence size of seven amino acid residues was required for a high antimicrobial activity against Pseudomonas aeruginosa. The insertion of additional arginine and tryptophan residues into the peptides resulted only in small variations in the antimicrobial activity, whereas replacement of a tryptophan residue with tyrosine in the hepta- and hexapeptides resulted in reduced antimicrobial activity, especially against the Gram-negative bacteria. The peptides were non-haemolytic, making them highly potent as prospective antibiotic agents.     

Peptidome analysis reveals the involvement of endogenous peptides in mouse pancreatic dysfunction with aging

Type 2 diabetes (T2D) is a glucose regulation disorder that has significantly enhanced mortality and the global disease burden. The prevalence of T2D has increased worldwide and is higher in the elderly. The function of pancreatic islets decreases with age, which is one important reason for the occurrence of diabetes in the elderly. Recently, peptidome analysis has attracted attention. However, the role of age-related peptides in pancreatic dysfunction has not been investigated extensively. Here, we conducted a comparison of endogenous peptides between pancreas from adult and aging mice by liquid chromatography tandem mass spectrometry (LC-MS/MS). A total of 2,089 peptides originating from 1,280 protein precursors were identified, of which 232 were upregulated and 183 were downregulated in the aging mice (fold change ≥ 2 and p < 0.05), suggesting that the expression of pancreatic peptides in mice varied with age. The molecular weight of most peptides was <3.0 kDa, and the isoelectric point distribution had a bimodal characteristic. Further analysis of cleavage site patterns indicated that proteases cleaved pancreatic proteins according to their rules. Moreover, Gene Ontology and pathway analyses showed that the differentially expressed peptides potentially had specific effects on pancreatic dysfunction. Some differential peptides were located within the domains of precursor proteins that were closely associated with the development of diabetes. We believe that our research may advance the current understanding of pancreas-derived peptides and that certain peptides may be involved in the etiology of diabetes.     

Characterization of bioactive peptides in bovine adrenal medulla by a combination of fast HPLC and ESI-MS

A method based upon a combination of fast high-performance liquid chromatography (HPLC) and electrospray ionization (ESI)–mass spectrometry (MS) is developed for the analysis of bioactive peptides in bovine adrenal medulla. The fast HPLC uses a short column (33 mm×4.6 mm) packed with nonporous silica-based C-18 stationary phase. Prior to HPLC separation, the medulla was homogenized and the peptide-rich fraction was isolated from it by solid-phase extraction. In-source collision-induced dissociation and tandem MS were used to obtain the sequence of the suspected peptides. Several peptides, including Met–Enk, Leu–Enk, Leu–Enk–Lys, bovine adrenal medullary (BAM)-12 (Met–Enk–RRVGRPE), Leu–Enk–Arg, and YGGT, were unambiguously identified. The first four peptides are the products of proenkephalin A precursor protein and Leu–Enk–Arg belongs to the dynorphin family and is derived from proenkephalin B (prodynorphin) precursor. The database search revealed that YGGT is a part of the sequence of five different precursor proteins.     

Mass spectrometry in plant proteomic analysis

Abstract

The current revolution in proteomics has been generated by the combination of very sensitive mass spectrometers coupled to microcapillary liquid chromatography, specific proteolysis of protein mixtures and software that is capable of searching vast numbers of mass measurements against predicted peptides from sequenced genomes. The challenges of post‐genomic plant biology include characterization of protein function, post‐translational modifications and composition of protein complexes as well as deciphering protein complements in intracellular compartments – proteomes of cell organelles. In this review we summarize the current mass spectrometry methods currently being used in plant proteomics and discuss the various tagging strategies that are being used for purification and proteomic analysis of plant protein complexes.

Abbreviations: BCCD, biotin carboxyl carrier protein domain; CBP, calmodulin‐binding protein; CID, collision‐induced dissociation; ESI, electrospray ionization; EST, expressed sequence tag; FT‐ICR, Fourier transform ion cyclotron resonance; GFP, green fluorescent protein; GST, glutathione S‐transferase; HA, haemagglutinin; HILEP, hydroponic isotope labelling of entire plants; His, histidine; HPB, HA–PreScission–Biotin; HPLC, high‐performance liquid chromatography; ICAT, isotope‐coded affinity tags; ICPL, isotope‐coded protein label; iTRAQ, isobaric tag for relative and absolute quantification; LC, liquid chromatography; MALDI, matrix‐assisted laser desorption ionization; MBP, maltose‐binding protein; MS, mass spectrometry; SDS‐PAGE, sodium dodecyl sulphate‐polyacrylamide gel electrophoresis; SILAC, stable isotope labelling with amino acids in cell culture; SILIP, stable isotope labelling in planta; Strep, streptavidin; TAP, tandem affinity purification; TBP, TATA‐box‐binding protein; TOF, time‐of‐flight; UPLC, ultraperformance liquid chromatography     

Rapid enrichment of bioactive milk proteins and iterative, consolidated protein identification by multidimensional protein identification technology

Direct injection of complex protein mixtures, e.g. those derived from crude biological fluids, is often incompatible with conventional LC supports, because of column clogging and rapid deterioration of chromatographic performance. In this paper, we report the use of restricted access media to rapidly enrich and fractionate human breast milk. This resin, combining size exclusion and anion exchange functionalities, yielded a fraction enriched in soluble CD14 and showing specific sCD14-dependant activity. This fraction was split into five aliquots, which were individually characterized using multidimensional protein identification technology. Reproducibility of the results was addressed by analysing and comparing five datasets using different protein identification tools available within the Sequest software. Furthermore, a comparison of three major releases of the Ensembl human protein database was performed to examine the effect of database updates on our results. We report here the benefit of repeated analysis of aliquots of the same fraction: first to increase the confidence in peptide identification by repeated confirmation in several aliquots; and second to assess experimental reproducibility. We demonstrate furthermore the effect of database modifications on the results and the importance of constantly re-analysing data with new releases to keep them consistent and up to date with the latest protein identities and predictions available.     

Preparation,isolation and identification of iron-chelating peptides derived from Alaska pollock skin

Alaska pollock skin as aquatic by-product was usually discarded in food processing. Iron deficiency has been a nutritional problem for a long period. In this study, Alaska pollock skin was used to generate iron-chelating peptides after being treated by commercial enzymes. Sequential chromatography, including immobilized metal affinity chromatography (IMAC) and reversed phase high performance liquid chromatography (RP-HPLC), was used for capturing and purifying iron-chelating peptides. One tripeptide, with high iron-chelating activity, was obtained and identified by electrospray ionization tandem mass spectrometry (LC–ESI-MS/MS). The amino acid sequence of the iron-chelating peptide was identified to be Ser-Cys-His (MW: 345 Da). These results show that Alaska pollock skin could be utilized to generate iron-chelating peptides as an iron supplement in functional food industry.     

Mechanism of translational regulation by miR-2 from sites in the 5' untranslated region or the open reading frame

MicroRNAs (miRs) commonly regulate translation from target mRNA 3' untranslated regions (UTRs). While effective miR-binding sites have also been identified in 5' untranslated regions (UTRs) or open reading frames (ORFs), the mechanism(s) of miR-mediated regulation from these sites has not been defined. Here, we systematically investigate how the position of miR-binding sites influences translational regulation and characterize their mechanistic basis. We show that specific translational regulation is elicited in vitro and in vivo not only from the 3'UTR, but equally effectively from six Drosophila miR-2-binding sites in the 5'UTR or the ORF. In all cases, miR-2 triggers mRNA deadenylation and inhibits translation initiation in a cap-dependent fashion. In contrast, single or dual miR-2-binding sites in the 5'UTR or the ORF yield rather inefficient or no regulation. This work represents the first demonstration that 5'UTR and ORF miR-binding sites can function mechanistically similarly to the intensively investigated 3'UTR sites. Using single or dual binding sites, it also reveals a biological rationale for the high prevalence of miR regulatory sites in the 3'UTR.     

Impact of sequence on the molecular assembly of short amyloid peptides

The goal of this work is to understand how the sequence of a protein affects the likelihood that it will form an amyloid fibril and the kinetics along the fibrillization pathway. The focus is on very short fragments of amyloid proteins since these play a role in the fibrillization of the parent protein and can form fibrils themselves. Discontinuous molecular dynamics simulations using the PRIME20 force field were performed of the aggregation of 48‐peptide systems containing SNQNNF ( PrP (170–175 )), SSTSAA (RNaseA(15–20)), MVGGVV (Aβ(35–40)), GGVVIA (Aβ(37–42)), and MVGGVVIA (Aβ(35–42)). In our simulations SNQQNF, SSTTSAA, and MVGGVV form large numbers of fibrillar structures spontaneously (as in experiment). GGVVIA forms β‐sheets that do not stack into fibrils (unlike experiment). The combination sequence MVGGVVIA forms less fibrils than MVGGVV, hindered by the presence of the hydrophobic residues at the C‐terminal. Analysis of the simulation kinetics and energetics reveals why MVGGVV forms fibrils and GGVVIA does not, and why adding I and A to MVGGVVIA reduces fibrillization and enhances amorphous aggregation into oligomeric structures. The latter helps explain why Aβ(1–42) assembles into more complex oligomers than Aβ(1–40), a consequence of which is that it is more strongly associated with Alzheimer's disease. Proteins 2014; 82:1469–1483. © 2014 Wiley Periodicals, Inc.     

Vectors with rare-cutter restriction enzyme sites for expression of open reading frames in transgenic plants

Cloning of long open reading frames (ORFs) into plant gene expression vectors and transfer of the chimeric expression cassettes into binary vectors is often hampered by the presence of restriction enzyme cleavage sites internal to the open reading frame (ORF) to be expressed. We therefore modified the commonly used expression vector pRT100 [7] and several pGPTV binary vectors [2] by replacing 6 bp restriction sites with 8 bp sequences recognized by rare-cutter restriction enzymes.