Sequence Of Amino Acid Residues Research Articles

Proteomics

Proteomics is a branch of molecular biology that deals with the identification and quantification of proteins in living objects, as well as the analysis of protein functions and their interactions.
 Proteomics is studied by proteins that are expressed in a given cell, tissue or organism over a period of time (under certain conditions).
 It is known that information about the primary structure of a protein (the sequence of amino acid residues in a protein) is contained in a structural gene in the form of a codon sequence (genetic code). On the other hand, less than 10% of genes are functionally active (expressed) in the somatic cells of our body. Moreover, a distinct tissue-specific expression of genes is observed. This, in turn, leads to the peculiarities of the qualitative composition of the synthesized proteins in various tissues. No less important is the fact that the total amount of proteins synthesized by our tissues is much greater than the total number of structural genes containing information about their original structure. This phenomenon is explained by the activity of such mechanisms as alternative splicing and a wide variety of post-translational peptide processing pathways (covalent modification of a polypeptide synthesized on the ribosome) in health and disease. Thus, even a brief review of the semantic content of the term "proteomics" indicates an extremely complex system of protein molecules in our body, which plays a fundamental role in maintaining homeostasis and is involved in the formation of adaptive responses in response to adverse changes in the internal and external environment.

Different directions for retro-inverso peptides.

Retro-inverso peptides are reversed sequences of mirror-image amino acid residues. Synthetic molecules of this type have long been considered potential mimics of functional peptides. This Peptide Highlights article examines some recent applications of the retro-inverso transformation at the interface of peptide chemistry and medicine.

Non-canonical proline-tyrosine interactions with multiple host proteins regulate Ebola virus infection.

The Ebola virus VP30 protein interacts with the viral nucleoprotein and with host protein RBBP6 via PPxPxY motifs that adopt non-canonical orientations, as compared to other proline-rich motifs. An affinity tag-purification mass spectrometry approach identified additional PPxPxY-containing host proteins hnRNP L, hnRNPUL1, and PEG10, as VP30 interactors. hnRNP L and PEG10, like RBBP6, inhibit viral RNA synthesis and EBOV infection, whereas hnRNPUL1 enhances. RBBP6 and hnRNP L modulate VP30 phosphorylation, increase viral transcription, andexert additive effects on viral RNA synthesis. PEG10 has more modest inhibitory effects on EBOV replication. hnRNPUL1 positively affects viral RNA synthesis but in a VP30-independent manner. Binding studies demonstrate variable capacity of the PPxPxY motifs from these proteins to bind VP30, define PxPPPPxY as an optimal binding motif, and identify the fifth proline and the tyrosine as most critical for interaction. Competition binding and hydrogen-deuterium exchange mass spectrometry studies demonstrate that each protein binds a similar interface on VP30. VP30 therefore presents a novel proline recognition domain that is targeted by multiple host proteins to modulate viral transcription.

Effect of Favipiravir on some epidemic infections: A mini review

Favipiravir is a modern antiviral drug that can be used in developing viral pandemics, such as the Ebola virus, H1N1 flu, Lassa fever, and haemorrhagic fever outbreaks in Argentina in 2009. A. Chain conclusion Favipiravir is transformed to favipiravir-RTP and inserted into the RNA strand that is elongating. Then, since favipiravir acts as a chain terminator, chain elongation slows down at incorporation site of favipiravir and does not continue. The proofreading enzyme cannot repair this complex of RNA-favipiravir and it will be discarded as excessive RNA, which causes the extinction of the viral genome. Mutagenesis with lethal consequences Ribavirin is used in the RNA elongating process until completion. The single strand of RNA with several ribavirin incorporation sites incorporates ribavirin or acts as mRNA for the production of viral proteins. Due to incorporation of ribavirin onto viral RNA, a mismatching of the base pairs (transition mutation) will occur. Translation of this mutated RNA will then cause mutations in the sequence of amino acid residues of the protein, result in impaired of protein function. Viral proteins that have lost their function are unable to replicate or generate infectious viral particles, and the virus is no longer infectious. As a result, lethal mutagenesis ends viral infection in a different way than chain termination. Favipiravir’s clinical trial against Ebola virus-infected patients has not yet been formally approved, and further research is required. Favipiravir, on the other hand, poses a risk of embryo toxicity and teratogenicity. As a result, the Japanese Ministry of Health, Welfare and Labor have been approved this medication with recommendations for more clinical use until August 15, 2014, when they approved the use of favipiravir due to the Ebola virus epidemic in West Africa. The aim of this review is to investigate the potential impact of favipiravir on infections espectially RNA-virus infections, according to previous published investigations, and thus to encourage rapid approval of this interesting antivirus in emergencies.

A Novel Fast and Efficient Approach to Purify the Thrombin-like Enzyme from Two <i>Bothrops</i>-genus Snake Venoms

Snake venoms are important sources of complex substances with a variety of pharmacological activities. Among them serine proteinases (SVSPs) have important effects on the hemostatic system influencing the hemodynamic of human or animal blood. Bothrops genus-snake venoms are rich in the thrombin-like enzyme, a type of SVSPs, with great interest to produce medicine. Therefore, the aim of this work was to describe a rapid, only two-step chromatographic-procedure developed to perform a faster purification of SVSPs from Bothrops alternatus and Bothrops moojeni venoms. As a result, two groups of serine proteinases respectively BaIII-4 - 8 and BmIII-2 - 5, were isolated and their molecular masses estimated by mass spectrometry and SDS-PAGE under denaturing conditions. The SVTLEs isolated from B. alternatus (BaIII-3 - 8) and B. moojeni (BmIII-2 - 5) fractions displayed apparent molecular mass around 30-40 kDa which closely relates to SVTLEs from other Bothrops species, as well their amino acid partial sequence triptych ions. Analysis of the alignment of the amino acid residue sequences of the N-terminal of the isolated proteins revealed a high level of identity with other SVTLEs. These enzymes coagulated plasma and showed fibrinogenolytic activity in blood. These SVTLEs isolated can be considered α-fibrinogenase mainly due to the fact that they hydrolyze the Aα chain fibrinogen. B. moojeni SVTLE showed greater activity than those from B. alternatus isolated. This new purification alternative approach developed was faster and more economical than the traditional process currently used. Faster purification and improved extraction yield can provide new insights into these enzymes including the use as a candidate molecule in the production of new drugs.

ABCA7 links sterol metabolism to the host defense system: Molecular background for potential management measure of Alzheimer's disease.

ATP-binding cassette transporter (ABC) A7 is a membrane protein that belongs to the large family of ABC transporters. It is 54% homologous in amino acid residue sequence to ABCA1 which mediates biogenesis of plasma high density lipoprotein (HDL) from cellular phospholipid and cholesterol with extracellular helical apolipoproteins such as apolipoprotein (apo) A-I. When transfected and expressed, ABCA7 also mediates generation of HDL-like particles but small and of less cholesterol content. However, endogenous ABCA7 is unlikely involved in HDL biogenesis and rather to regulate the host-defense system such as phagocytotic function of the cells. ABCA1 expression is regulated by cellular cholesterol levels, positively by the liverXreceptor (LXR) in extrahepatic peripheral cells. However, it is modulated dually in the liver being relevant to transport of cholesterol for its catabolism; positively by LXR and negatively by sterol regulatory element binding protein (SREBP) or hepatic nuclear factor 4α (HNF4α). In contrast, ABCA7 expression was shown to be regulated negatively by the SREBP system so that decrease of cell cholesterol enhances ABCA7 function such as cellular phagocytotic reaction, suggesting that it links cholesterol metabolism to the host defense system. The interest is being build up in ABCA7 as its genomic diversity has been found related to a risk for late-onset Alzheimer's diseases. More recent findings indicate that ABCA7 is involved in metabolism of amyloid β peptide including its phagocytotic clearance. Accordingly, modulation of ABCA7 activity by manipulating cholesterol metabolism may open a new path for management of Alzheimer's disease.

A Novel Reversibly Glycosylated Polypeptide-2 of Bee Pollen from Rape (Brassica napus L.): Purification and Characterization.

Reversibly glycosylated polypeptide (RGP), a kind of hydrosoluble and plasmodesmal-associated protein found in plants, plays a crucial role in the development of pollen. A novel RGP 2 was isolated and identified from rape (Brassica napus L.) bee pollen. RGP2 was isolated and purified by ion-exchange column and gel filtration chromatography, and characterized by MALDI-TOF-MS, LC-MS, immunological histological chemistry, and transmission electron microscope. Our results indicated that the RGP2 is an acidic protein (pI=5.46) with the molecular weight 42388 Da. It contained 17 kinds of amino acids, among which aspartic acid had the highest amount (71.56 mg/g). Homologous alignment of amino acid sequence results showed that RGP2 was 80.33%, 85.02%, 86.06%, and 88.93% identical to Arabidopsis thaliana RGP2 (AtRGP2), Oryza sativa RGP (OsRGP), Triticum aestivum RGP (TaRGP), and Zea maize RGP (ZmRGP), respectively. The localization results showed that RGP2 in rape anther existed in exine and intine of anther cells of rape flower by immunological histological chemistry and the subcellular localization identified that RGP2 appeared around the Golgi apparatus in cytoplasm by transmission electron microscope. RGP2 has a highly conserved sequence of amino acid residues and potential glycosylation sites.

Computer Modeling of N-Acetylglutamate Synthase: From Primary Structure to Elemental Stages of Catalysis

Three-dimensional full-atom model of the enzyme complex with acetyl-CoA and substrate was constructed on the basis of the primary sequence of amino acid residues of N-acetyl glutamate synthase. Bioinformatics approaches of computer modeling were applied, including multiple sequence alignment, prediction of co-evolutionary contacts, and ab initio folding. On the basis of the results of calculations by classical molecular dynamics and combined quantum and molecular mechanics (QM/MM) methods, the structure of the active site and the reaction mechanism of N-acetylglutamate formation are described. Agreement of the structures of the enzyme-product complexes obtained in computer modeling and in the X-ray studies validates the reliability of modeling predictions.

The use of knowledge management tools in viroinformatics. Example study of a highly conserved sequence motif in Nsp3 of SARS-CoV-2 as a therapeutic target

Knowledge management tools that assist in systematic review and exploration of scientific knowledge generally are of obvious potential importance in evidence based medicine in general, but also to the design of therapeutics based on the protein subsequences and fold motifs of virus proteins as considered here. Rapid access to bundles (clusters) of related elements of knowledge gathered from diverse sources on the Internet and from growing knowledge repositories seem particularly helpful when exploring less obvious therapeutic targets in viruses (for which knowledge new to the researcher is important), and when using the following concept. Subsequences of amino acid residue sequences of proteins that are conserved across strains and species are (a) more likely to be important targets and (b) less likely to exhibit escape mutations that would make them resistant to vaccines and therapeutic agents. However, the terms “conserved” and even “highly conserved” used by authors are matters of degree, depending on how distant from SARS-CoV-2 they wished to go in comparing other sequences. The binding site to the human ACE2 protein as virus receptor and human antibody CR3022 binding site on the spike glycoprotein are rather variable by the criteria used in the present and preceding studies. To look for more strongly conserved targets, open reading frames of SARS-CoV-2 were examined for extremely highly conserved regions, meaning recognizable across many viruses and organisms. Most prominent is a motif found in SARS-CoV-2 non-structural protein 3 (Nsp3). It relates to a fold called type called the macro domain and has remarkably wide distribution across organisms including humans with significant homologies involving three especially conserved subsequences (a) VVVNAANVYLKHGGGVAGALNK, (b) LHVVGPNVNKG, and (c) PLLSAGIFG. Careful study of the variations of these and of the more variable sequences between and around them might provide a finer “scalpel” to ensure inhibition of a vital function of the virus without impairing the functions of related host macro domains.

Синтез и анализ зависимости анксиолитического эффекта от структуры лейцилтриптофановых лигандов 18 кДа транслокаторного белка

Ранее в НИИ фармакологии имени В. В. Закусова с использованием оригинальной стратегии создания фармакологически активных дипептидов на основе структур непептидных лекарственных средств получены дипептидные лиганды 18 кДа транслокаторного белка (TSPO), амид N-карбобензокси-L-триптофанил-L-изолейцина (ГД-23) и амид N-фенилпропионил-L-триптофанил-L-лейцина (ГД-102), проявившие анксиолитическую активность в стандартных тестах. В настоящей работе получены аналоги дипептида ГД-102 с обратной последовательностью аминокислотных остатков: метиламид N-фенилпропионил-L-лейцил-L-триптофана (ГД-140), N-фенилпропионил-L-лейцил-L-триптофан (ГД-139), амид N-фенилацетил-L-лейцил-L-триптофана (ГД-141), метиловый эфир N-фенилпропионил-L-лейцил-L-триптофана (ГД-138), амид N-фенилпропионил-L-лейцил-L-триптофана (ГД-136). Исследование в тесте «Открытое поле» (ОП) на мышах при внутрибрюшинном введении показало, что вновь синтезированные дипептиды уступают по активности ГД-102 (0,01 – 0,1 мг/кг). Дипептид ГД-140 проявлял анксиолитическую активность в дозах 0,1, 0,5, 1 мг/кг; ГД-139 в дозах 0,5 и 5 мг/кг; ГД-141 в дозах 1 и 5 мг/кг. Дипептид ГД-138 в дозе 0,1 мг/кг снижал двигательную активность животных в ОП. ГД-136 не проявил активность в интервале доз 0,1 – 5 мг/кг. Молекулярный докинг продемонстрировал возможность размещения изученных соединений в зоне связывания лиганда PK11195 с TSPO (PDB ID: 2MGY). При этом для ГД-136, ГД-139, ГД-140 и ГД-141 выявлено наличие pi-стэкинга фенильного фрагмента молекулы с Trp107 рецептора. У ГД-140 и ГД-102 выявлен еще и pi-стэкинг с Trp95. У ГД-138 pi-стэкинг отсутствовал как с Trp107, так и с Trp95. Сделано заключение о том, что ключевым взаимодействием, влияющим на проявление анксиолитической активности, является pi-стэкинг дипептидного лиганда с Trp95 рецептора, а последовательность Trp-Leu для дипептидных лигандов TSPO предпочтительнее последовательности Leu-Trp.

Multiple Diversity of Mitochondrial Cytochrome b Amino Acid Sequences of the Same Length in Animals.

The size of natural peptide molecules (proteins) can be considered as the number of amino acid residues p (protein length). The aim of the work was to analyze the region of existence and occurrence of natural amino acid residue sequences formed as a result of matrix synthesis on the p scale. The object of the study was the Swiss-Prot database consisting of more than 5.6 × 105 primary peptide structures, which were fully determined (complete sequence). Sequences containing non-standard amino acid residues, as well as identical copies of sequences, were removed from them. The remaining 463,450 different sequences with a length of 2–35,213 residues were used for further analysis. It was shown that the protein lengths of different biological domains and kingdoms are characterized by different regions of existence, and the profile shapes of the obtained curves are close to a number of known distributions. At the same time, they have sharp high peaks, indicating the existence of a large number of specific molecules with the same protein length. One of these peaks characterizes more than 1,000 different sequences of mitochondrial cytochrome b molecules at p = 379. Such examples may indicate that the most perfect protein lengths were selected in the evolutionary process to perform this function. As a result, many protein molecules with different sequences of the same length and characterized by the same functions were formed.

Bioinformatics studies on a function of the SARS-CoV-2 spike glycoprotein as the binding of host sialic acid glycans

SARS-CoV and SARS-CoV-2 do not appear to have functions of a hemagglutinin and neuraminidase. This is a mystery, because sugar binding activities appear essential to many other viruses including influenza and even most other coronaviruses in order to bind to and escape from the glycans (sugars, oligosaccharides or polysaccharides) characteristic of cell surfaces and saliva and mucin. The S1 N terminal Domains (S1-NTD) of the spike protein, largely responsible for the bulk of the characteristic knobs at the end of the spikes of SARS-CoV and SARS-CoV-2, are here predicted to be “hiding” sites for recognizing and binding glycans containing sialic acid. This may be important for infection and the ability of the virus to locate ACE2 as its known main host cell surface receptor, and if so it becomes a pharmaceutical target. It might even open up the possibility of an alternative receptor to ACE2. The prediction method developed, which uses amino acid residue sequence alone to predict domains or proteins that bind to sialic acids, is naïve, and will be advanced in future work. Nonetheless, it was surprising that such a very simple approach was so useful, and it can easily be reproduced in a very few lines of computer program to help make quick comparisons between SARS-CoV-2 sequences and to consider the effects of viral mutations.

Molecular insights and immune responses of big belly seahorse syndecan-2 (CD362): Involvement of ectodomain in regulating cell survival, proliferation, and wound healing

Syndecan-2, also known as CD362, is a transmembrane heparan sulfate proteoglycan which regulates cell growth, proliferation, cell adhesion, wound healing, and recruits immune cells. In the present study, we performed bioinformatics, spatial and temporal expression analyses of Hippocampus abdominalis syndecan-2 (HaSDC-2). Additionally, functional assays were conducted. HaSDC-2 has five major domains; an extracellular heparan sulfate attachment domain, a co-receptor binding domain, a transmembrane domain, two conserved domains (C1 domain, C2 domain), and a variable (V) domain. The ectodomain contained a signal peptide and GAG attachment sites. In-silico analysis revealed that HaSDC-2 contained a 798 bp long ORF and protein sequence of 265 amino acid residues. Further analysis of the amino acid sequence predicted a 28.9 kDa molecular weight and a 4.13 theoretical isoelectric point. The spatial expression of HaSDC-2 was ubiquitous in all tested tissues. HaSDC-2 expression in the liver was upregulated 24 h post-injection in response to all stimuli. Further, HaSDC-2 expression in blood cells was upregulated at 12 and 72 h post-injection in response to all the stimuli. HaSDC-2 + pcDNA™3.1(+) transfected cells exhibited significant survival in response to cell stressors such as H2O2 and HED. The ectodomain of recombinant HaSDC-2 treated cells showed significant cell proliferation in a concentration-dependent manner. The scratch wound healing assay showed significant Δ gap closures with increasing concentrations of HaSDC-2. Collectively, these results indicated that syndecan-2 was involved in regulating immune responses and cell stress conditions.

Changes in the nociceptive response to thermal stimulation in rats following administration of N-terminal analogs of the adrenocorticotropic hormone

Melanocortins (MCs) are an increasingly studied class of regulatory peptides exerting a wide range of biological effects. All naturally occurring MCs share a His-Phe-Arg-Trp fragment (HFRW) corresponding to the sequence of amino acid residues 6–9 of the adrenocorticotropic hormone (ACTH6-9), which is also a central active component of ACTH. Attaching the Pro-Gly-Pro (PGP) sequence to the C-end of the peptide extends the duration of the peptide’s effect. The aim of this study was to investigate the effects of ACTH6-9-PGP (HFRWPGP) on the spinal and supraspinal mechanisms involved in the nociceptive response in rats and to compare them to those of its structural analog ACTH4-7-PGP (MEHFPGP). ACTH6-9-PGP effects were studied following the intraperitoneal administration of the peptide at doses 0.5, 1.5, 5, 15, 50, 150, or 450 μg/kg 15 minutes before the hot plate and tail flick tests. ACTH4-7-PGP effects were studied under the same conditions at the following doses: 50, 150 and 450 μg/kg. We found that ACTH6-9-PGP administered intraperitoneally at 5 or 150 μg/kg induced a pronounced reduction in pain sensitivity 15 and 45 minutes after the injection (p = 0.04); this effect was implemented via supraspinal mechanisms. In the tail flick test, 150 μg/kg ACTH6-9-PGP increased pain sensitivity, with the participation of segmental spinal mechanisms (p = 0.04). ACTH4-7-PGP did not have any effect on the studied mechanisms of pain sensitivity. Thus, unlike ACTH4-7-PGP, ACTH6-9-PGP can both increase pain sensitivity and exert an analgesic effect.

An Improved Program for the Estimation of Protein Theoretical Relative Molecular Mass and Uncertainty.

Presented here is the National Institute of Standards and Technology (NIST) Mass Calculator, a software tool that provides both a relative molecular mass (Mr) value and an associated uncertainty value for a given protein sequence. The calculation of a protein Mr based on its amino acid residue sequence is performed by many software applications. Unfortunately, many of the results do not agree with each other. Reasons for this lack of consensus may include the use of rounded values, calculation errors, or alternative calculation methods, and it is often not possible to distinguish the source of the differences. Additionally, the result is provided without an estimate of precision. This would imply that the Mr is perfectly known when in fact it is not because the basis for the calculation, either the relative atomic masses or the standard atomic weights, are themselves provided as estimates. Until the release of the NIST Mass Calculator, there were no applications available to provide both an Mr value and an associated uncertainty value. Furthermore, the full disclosure of the computation methods and elemental values allows for independent verification of the results. The uncertainty is obtained via Monte Carlo simulation and is now a useful feature in light of the high resolution capability now available in the mass spectrometry of intact proteins.

A novel antimicrobial protein of the endophytic Bacillus amyloliquefaciens and its control effect against Fusarium chlamydosporum

Fusarium chlamydosporum is the causal agent of stem rot in Jacaranda acutifolia. Bacillus amyloliquefaciens is an endophytic bacterium that shows promising biological control activity against F. chlamydosporum. In this study, B. amyloliquefaciens was cultured in a fermentation broth, and the main antimicrobial substance in the fermentation broth was isolated using the ammonium sulfate precipitation method and purified by DEAE sepharose fast flow weak anion exchange chromatography and sephadex G-50 molecular sieve chromatography. Polyacrylamide gel electrophoresis revealed a single antimicrobial protein with a molecular weight of approximately 29.0 kDa. The antimicrobial protein is a strong antagonist against F. chlamydosporum, leading to mycelial deformity, unclear mycelial septa, and isolated and granulated intracellular protoplasm. The N-terminal eight-amino acid sequence, NH2-Gly-Arg-Pro-Leu-Pro-Leu-Ala-Ala, was determined using the automatic Edman degradation method. BLAST analysis indicated that the amino acid residue sequence at positions 154–161 shows 100% homology to the hypothetical protein of Chromobacterium sp. LK1. However, no known homologous antimicrobial protein was identified, indicating that we have isolated a novel antimicrobial protein.

Observation of a weak intra-residue C5 hydrogen-bond in a dipeptide containing Gly-Pro sequence.

Specific folded structures of peptides and proteins depend on the sequence of various amino acid residues as well as different types of noncovalent interactions induced by the backbone as well as side-chains of those residues. In general, secondary structures of peptides and proteins are stabilized by C6 (δ-turn), C7 (γ-turn), C10 (β-turn), C13 (α-turn), and C15 (π-turn) hydrogen-bonded rings formed through inter-residue interactions. However, it has been reported recently that an intraresidue C5 hydrogen-bond, which is relatively weak in strength, can contribute significantly to the stability of peptides and proteins. The C5 hydrogen-bond is mostly present in the β-sheet structures of peptides and proteins along with other inter-residue noncovalent interactions. In this work, we have studied structures and conformational preferences of a dipeptide Z-Gly-Pro-OH (Z = benzyloxycarbonyl) using mass-selected vibrationally resolved electronic spectroscopy and IR-UV double resonance spectroscopy coupled with quantum chemistry calculations. Two conformers of the peptide are observed in the experiment. One of the conformers has an extended β-strand type structure stabilized by C5 hydrogen-bonding, while the other one is folded through O-H ⋯ π interaction. The noncovalent interactions present in the two observed structures of the peptide are validated by natural bond orbital and noncovalent interaction calculations.

Epitope matching in kidney transplantation: recent advances and current limitations.

Evolution of human leukocyte antigen (HLA) molecular typing techniques has progressively enabled more accurate determination of the three-dimensional building blocks that form the antibody accessibility and binding sites of each HLA allele. These immunogenic HLA regions known as epitopes are composed of polymorphic sequences of amino acid residues termed eplets. This review provides a critical appraisal of the current understanding of epitope compatibility in kidney transplantation. There is a tendency to suggest that epitope matching is likely to be superior to broad antigen HLA matching such that the allocation of donor kidneys to patients with a more favorable epitope compatibility profile may lead to better allograft outcomes. A growing body of work has highlighted the association between a greater number of eplet mismatches and adverse allograft outcomes, and approaches using eplet matching have been successfully implemented in organ allocation programs. However, our understanding of epitope compatibility remains in its infancy, requiring further and more in-depth evaluation. Critically, it remains unclear how best to translate findings derived at the population level to the care of individual patients. Questions that need to be answered include a lack of consensus in the definition and interpretation of epitope compatibility, are class I and II compatibility of similar clinical importance, how best to define predetermined mismatch thresholds for utilization in organ allocation, and whether other properties such as differences in electrostatic potential between donor and recipient HLA alleles are also important in determining immunological compatibility. Epitope matching likely represents a valid progression in understanding donor-recipient HLA compatibility. However, more clinical data and a better understanding about differences in methods to determine epitope compatibility are required before the approach can be widely applied in clinical practice.

Transcriptome-based Discovery of AP2/ERF tRanscription Factors and Expression Profiles Under Herbivore Stress Conditions in Bamboo (Bambusa emeiensis)

Bambusa emeiensis is one of the most economically important bamboos, yet the yield and quality of this bamboo species continue to be challenged by insect herbivores. APETALA2/ethylene responsive factors (AP2/ERF) comprise a large family of plant transcription factors regulating numerous biological processes and playing critical roles in plant defence responses. In the present study, 47 AP2/ERF genes were identified and classified in the B. emeiensis herbivore-induced transcriptome. Based on AP2 domain numbers, conserved amino-acid residues, motif analyses and phylogenetic trees and BeAP2/ERF proteins were grouped into four subfamilies, namely AP2, ERF, Dehydration-responsive-element-binding (DREB) and Soloist, and these subfamilies consisted of nine, 23, 14 and 1 proteins, respectively. Amino-acid residue sequences of the AP2 domain in B. emeiensis were conserved compared with those in Arabidopsis thaliana. Expression analyses revealed that the treatment (herbivore damage) and control groups exhibited different expression patterns, and majority of BeERF/DREB genes were significantly and differentially expressed in the transcriptome, as verified using quantitative real-time PCR (qPCR). Finally, eight genes were selected for further PCR analyses of tissue-specific expression, of which the four tissues exhibited different expression patterns. Our data indicated that the genes encoding the ERF/DREB subfamily of B. emeiensis play critical roles in its response to herbivores.

Roles of membrane transporters: connecting the dots from sequence to phenotype.

Plant membrane transporters are involved in diverse cellular processes underpinning plant physiology, such as nutrient acquisition, hormone movement, resource allocation, exclusion or sequestration of various solutes from cells and tissues, and environmental and developmental signalling. A comprehensive characterization of transporter function is therefore key to understanding and improving plant performance. In this review, we focus on the complexities involved in characterizing transporter function and the impact that this has on current genomic annotations. Specific examples are provided that demonstrate why sequence homology alone cannot be relied upon to annotate and classify transporter function, and to show how even single amino acid residue variations can influence transporter activity and specificity. Misleading nomenclature of transporters is often a source of confusion in transporter characterization, especially for people new to or outside the field. Here, to aid researchers dealing with interpretation of large data sets that include transporter proteins, we provide examples of transporters that have been assigned names that misrepresent their cellular functions. Finally, we discuss the challenges in connecting transporter function at the molecular level with physiological data, and propose a solution through the creation of new databases. Further fundamental in-depth research on specific transport (and other) proteins is still required; without it, significant deficiencies in large-scale data sets and systems biology approaches will persist. Reliable characterization of transporter function requires integration of data at multiple levels, from amino acid residue sequence annotation to more in-depth biochemical, structural and physiological studies.