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RATIONALE:There is increasing interest in methods of direct analysis mass spectrometry that bypass complex sample preparation steps. METHODS:One of the most interesting new ionisation methods is rapid evaporative ionisation mass spectrometry (REIMS) in which samples are vapourised and the combustion products are subsequently ionised and analysed by mass spectrometry (Synapt G2si). The only sample preparation required is the recovery of a cell pellet from a culture that can be analysed immediately. RESULTS:We demonstrate that REIMS can be used to monitor the expression of heterologous recombinant proteins in Escherichia coli. Clear segregation was achievable between bacteria harvesting plasmids that were strongly expressed and other cultures in which the plasmid did not result in the expression of large amounts of recombinant product. CONCLUSIONS:REIMS has considerable potential as a near-instantaneous monitoring tool for protein production in a biotechnology environment.

The majority of bacterial genomes have high coding efficiencies, but there are some genomes of intracellular bacteria that have low gene density. The genome of the endosymbiont Sodalis glossinidius contains almost 50 % pseudogenes containing mutations that putatively silence them at the genomic level. We have applied multiple ‘omic’ strategies, combining Illumina and Pacific Biosciences Single-Molecule Real-Time DNA sequencing and annotation, stranded RNA sequencing and proteome analysis to better understand the transcriptional and translational landscape of Sodalis pseudogenes, and potential mechanisms for their control. Between 53 and 74 % of the Sodalis transcriptome remains active in cell-free culture. The mean sense transcription from coding domain sequences (CDSs) is four times greater than that from pseudogenes. Comparative genomic analysis of six Illumina-sequenced Sodalis isolates from different host Glossina species shows pseudogenes make up ~40 % of the 2729 genes in the core genome, suggesting that they are stable and/or that Sodalis is a recent introduction across the genus Glossina as a facultative symbiont. These data shed further light on the importance of transcriptional and translational control in deciphering host–microbe interactions. The combination of genomics, transcriptomics and proteomics gives a multidimensional perspective for studying prokaryotic genomes with a view to elucidating evolutionary adaptation to novel environmental niches.

Major urinary proteins (MUP) are the major component of the urinary protein fraction in house mice (Mus spp.) and rats (Rattus spp.). The structure, polymorphism and functions of these lipocalins have been well described in the western European house mouse (Mus musculus domesticus), clarifying their role in semiochemical communication. The complexity of these roles in the mouse raises the question of similar functions in other rodents, including the Norway rat, Rattus norvegicus. Norway rats express MUPs in urine but information about specific MUP isoform sequences and functions is limited. In this study, we present a detailed molecular characterization of the MUP proteoforms expressed in the urine of two laboratory strains, Wistar Han and Brown Norway, and wild caught animals, using a combination of manual gene annotation, intact protein mass spectrometry and bottom-up mass spectrometry-based proteomic approaches. Cluster analysis shows the existence of only 10 predicted mup genes. Further, detailed sequencing of the urinary MUP isoforms reveals a less complex pattern of primary sequence polymorphism in the rat than the mouse. However, unlike the mouse, rat MUPs exhibit added complexity in the form of post-translational modifications, including the phosphorylation of Ser4 in some isoforms, and exoproteolytic trimming of specific isoforms. Our results raise the possibility that urinary MUPs may have different roles in rat chemical communication than those they play in the house mouse. Shotgun proteomics data are available via ProteomExchange with identifier PXD013986.

Background Reliable recognition of individuals requires phenotypic identity signatures that are both individually distinctive and appropriately stable over time. Individual-specific vocalisations or visual patterning are well documented among birds and some mammals, whilst odours play a key role in social recognition across many vertebrates and invertebrates. Less well understood, though, is whether individuals are recognised through variation in cues that arise incidentally from a wide variety of genetic and non-genetic differences between individuals, or whether animals evolve distinctive polymorphic signals to advertise identity reliably. As a bioassay to understand the derivation of individual-specific odour signatures, we use female attraction to the individual odours of male house mice (Mus musculus domesticus), learned on contact with a male’s scent marks. Results Learned volatile odour signatures are determined predominantly by individual differences in involatile major urinary protein (MUP) signatures, a specialised set of communication proteins that mice secrete in their urine. Recognition of odour signatures in genetically distinct mice depended on differences in individual MUP genotype. Direct manipulation using recombinant MUPs confirmed predictable changes in volatile signature recognition according to the degree of matching between MUP profiles and the learned urine template. Both the relative amount of the male-specific MUP pheromone darcin, which induces odour learning, and other MUP isoforms influenced learned odour signatures. By contrast, odour recognition was not significantly influenced by individual major histocompatibility complex genotype. MUP profiles shape volatile odour signatures through isoform-specific differences in binding and release of urinary volatiles from scent deposits, such that volatile signatures were recognised from the urinary protein fraction alone. Manipulation using recombinant MUPs led to quantitative changes in the release of known MUP ligands from scent deposits, with MUP-specific and volatile-specific effects. Conclusions Despite assumptions that many genes contribute to odours that can be used to recognise individuals, mice have evolved a polymorphic combinatorial MUP signature that shapes distinctive volatile signatures in their scent. Such specific signals may be more prevalent within complex body odours than previously realised, contributing to the evolution of phenotypic diversity within species. However, differences in selection may also result in species-specific constraints on the ability to recognise individuals through complex body scents. Electronic supplementary material The online version of this article (10.1186/s12915-018-0512-9) contains supplementary material, which is available to authorized users.

The Major Urinary Proteins (MUPs) of the house mouse, Mus musculus domesticus, are 18–19 kDa beta-barrel lipocalins that are involved in chemical communication between individuals. Many of them are excreted in urine where they play multiple roles, including coding of owner identity and transport, and slow release of bound volatile pheromones. One of them, darcin, is a pheromone in its own right and induces long-term memory for the identity and location of the scent mark owner. We have shown that mass spectrometric analysis of intact proteins, and their ion mobility behaviour, is capable of dissecting subtle structural differences between the members of this class of proteins. Moreover, mass spectrometric analysis of the intact proteins can contribute towards molecular phenotyping of MUPs. However, whilst allowing relative quantification, the ionisation propensity or gas phase properties of the individual MUPs may compromise absolute quantification. To solve the challenge of absolute quantification of MUP expression, we have designed and constructed a QconCAT built from endopeptidase LysC peptides that is capable of quantifying MUPs found in laboratory animal strains and some MUPs from wild caught individuals.

This article is part of a Special Issue “Chemosignals and Reproduction”. This paper reviews the role of chemosignals in the socio-sexual interactions of female mice, and reports two experiments testing the role of pup-derived chemosignals and the male sexual pheromone darcin in inducing and promoting maternal aggression. Female mice are attracted to urine-borne male pheromones. Volatile and non-volatile urine fractions have been proposed to contain olfactory and vomeronasal pheromones. In particular, the male-specific major urinary protein (MUP) MUP20, darcin, has been shown to be rewarding and attractive to females. Non-urinary male chemosignals, such as the lacrimal protein ESP1, promote lordosis in female mice, but its attractive properties are still to be tested. There is evidence indicating that ESP1 and MUPs are detected by vomeronasal type 2 receptors (V2R). When a female mouse becomes pregnant, she undergoes dramatic changes in her physiology and behaviour. She builds a nest for her pups and takes care of them. Dams also defend the nest against conspecific intruders, attacking especially gonadally intact males. Maternal behaviour is dependent on a functional olfactory system, thus suggesting a role of chemosignals in the development of maternal behaviour. Our first experiment demonstrates, however, that pup chemosignals are not sufficient to induce maternal aggression in virgin females. In addition, it is known that vomeronasal stimuli are needed for maternal aggression. Since MUPs (and other molecules) are able to promote intermale aggression, in our second experiment we test if the attractive MUP darcin also promotes attacks on castrated male intruders by lactating dams. Our findings demonstrate that the same chemosignal, darcin, promotes attraction or aggression according to female reproductive state

The majority of bacterial genomes have high coding efficiencies, but there are some genomes of intracellular bacteria that have low gene density. The genome of the endosymbiont Sodalis glossinidius contains almost 50% pseudogenes containing mutations that putatively silence them at the genomic level. We have applied multiple ‘omic strategies, combining: Illumina and Pacific Biosciences Single-Molecule Real Time DNA-sequencing and annotation; stranded RNA-sequencing; and proteome analysis to better understand the transcriptional and translational landscape of Sodalis pseudogenes, and potential mechanisms for their control. Between 53% and 74% of the Sodalis transcriptome remains active in cell-free culture. Mean sense transcription from Coding Domain Sequences (CDS) is four-times greater than that from pseudogenes. Comparative genomic analysis of six Illumina-sequenced Sodalis isolates from different host Glossina species shows pseudogenes make up ~40% of the 2,729 genes in the core genome, suggesting that they are stable and/or Sodalis is a recent introduction across the Glossina genus as a facultative symbiont. These data further shed light on the importance of transcriptional and translational control in deciphering host-microbe interactions. The combination of genomics, transcriptomics and proteomics give a multidimensional perspective for studying prokaryotic genomes with a view to elucidating evolutionary adaptation to novel environmental niches.ImportanceBacterial genes are generally 1Kb in length, organized efficiently (i.e. with few gaps between genes or operons), and few open reading frames (ORFs) lack any predicted function. Intracellular bacteria have been removed from extracellular selection pressures acting on pathways of declining importance to fitness and thus, these bacteria tend to delete redundant genes in favour of smaller functional repertoires. In the genomes of endosymbionts with a recent evolutionary relationship with their host, however, this process of genome reduction is not complete; Genes and pathways may be at an intermediate stage, undergoing mutation linked to reduced selection and small population numbers being vertically transmitted from mother to offspring in their hosts, resulting in an increase in abundance of pseudogenes and reduced coding capacities. A greater knowledge of the genomic architecture of persistent pseudogenes, with respect to their DNA structure, mRNA transcription and even putative translation to protein products, will lead to a better understanding of the evolutionary trajectory of endosymbiont genomes, many of which have important roles in arthropod ecology.

Previous investigations of the effects of clenbuterol have used suprapharmacological doses that induce myocyte death, alter muscle phenotype and do not approximate the proposed therapeutic dose for humans. Recently we reported that smaller doses of clenbuterol induce muscle growth without causing myocyte death. Here, we have used histochemical and proteomic techniques to investigate the molecular effects of this dose. Male Wistar rats (n = 6, per group) were infused with saline or 10 μg.kg-1.d-1 clenbuterol via subcutaneously implanted osmotic pumps. After 14 days the animals’ plantaris muscles were isolated for histochemical and proteomic analyses. Clenbuterol-induced significant muscle growth with concomitant protein accretion and preferential hypertrophy of fast oxidative glycolytic fibers. Clenbuterol reduced the optical density of mitochondrial staining in fast fibers by 20 % and the glycogen content of the muscle by 30 %. Differential analysis of two-dimensional gels showed that heat shock protein 72 and β-enolase were increased whereas aldolase A, phosphogylcerate mutase, and adenylate kinase decreased. Only heat shock protein 72 has previously been investigated in clenbuterol-treated muscles. In conclusion, the clenbutero linduced increase in muscle growth wass concomitant with qualitative changes in the muscle’s proteome that need to be considered when proposing therapeutic uses for this agent.

An appropriate level of water loss from eggs is critical to successful hatching. This water may be lost from the egg by evaporation, but where water loss is suboptimal, it is commonly observed that the hatchlings contain substantial amounts of a subcutaneous gel-like fluid. To characterize this fluid, we have analyzed the proteins that are contained within it. The protein complement comprised a small number of proteins in high concentrations. Proteomics analysis of the constituent proteins identified virtually all of these abundant proteins and confirmed that the subcutaneous gel was very similar in protein composition to plasma. However, the subcutaneous gel was substantially depleted of fibrinogen. It is possible that activation of the final stages of the coagulation process might account for the enhanced viscosity, creating a gel-like material that is relatively immobile in the subcutaneous space. This gel may function as a water volume that is partitioned during embryonic development in order to mitigate the effects of high water content of the egg caused by low mass loss during incubation and in some instances might also function as a water reserve to support the hatchling in the first few hours of life free of the shell.

A male-specific major urinary protein named darcin is attractive to female mice, Mus musculus, stimulates a learned attraction to volatile components of a male's urinary odour and induces spatial learning. In this article we show that darcin also induces learned attraction for a previously neutral olfactory stimulus (the odorant isoamyl acetate), acquired by repeated presentation of both stimuli together. We hypothesize that this is a case of olfactory–vomeronasal associative learning, in which darcin acts as the unconditioned reinforcer. However, the presence of darcin is not always attractive to adult female mice. Urine from males parasitized by the nematode Aspiculuris tetraptera has no attractive value for females, despite apparently normal presence of darcin. The loss of attractive value may be due to unknown infection-derived chemicals whose detection overrides the attraction induced by darcin, or prevents detection of darcin by other (unknown) mechanisms. Other cases in which male urine (and thus the presence of darcin) does not induce attraction are discussed, namely in lactating females, which respond with aggression towards intruder males, and in prepubertal females, which show aversive responses towards unfamiliar male urine. Thus, although the darcin sex pheromone induces attraction in adult female mice that does not need to be learned, such innate pheromonal responses can be modulated by the physiological or health status of the sender and receiver. This provides a degree of flexibility in response to pheromonal signals, but such that individuals of the same class or status still share consistent predictable responses to improve their reproductive fitness. Further, by readily inducing the same response towards other odorants through associative learning, pheromones can also target responses flexibly towards odour signatures at an individual-specific level.

BackgroundAmong invertebrates, specific pheromones elicit inherent (fixed) behavioural responses to coordinate social behaviours such as sexual recognition and attraction. By contrast, the much more complex social odours of mammals provide a broad range of information about the individual owner and stimulate individual-specific responses that are modulated by learning. How do mammals use such odours to coordinate important social interactions such as sexual attraction while allowing for individual-specific choice? We hypothesized that male mouse urine contains a specific pheromonal component that invokes inherent sexual attraction to the scent and which also stimulates female memory and conditions sexual attraction to the airborne odours of an individual scent owner associated with this pheromone.ResultsUsing wild-stock house mice to ensure natural responses that generalize across individual genomes, we identify a single atypical male-specific major urinary protein (MUP) of mass 18893Da that invokes a female's inherent sexual attraction to male compared to female urinary scent. Attraction to this protein pheromone, which we named darcin, was as strong as the attraction to intact male urine. Importantly, contact with darcin also stimulated a strong learned attraction to the associated airborne urinary odour of an individual male, such that, subsequently, females were attracted to the airborne scent of that specific individual but not to that of other males.ConclusionsThis involatile protein is a mammalian male sex pheromone that stimulates a flexible response to individual-specific odours through associative learning and memory, allowing female sexual attraction to be inherent but selective towards particular males. This 'darcin effect' offers a new system to investigate the neural basis of individual-specific memories in the brain and give new insights into the regulation of behaviour in complex social mammals.See associated Commentaryhttp://www.biomedcentral.com/1741-7007/8/71

SUMMARYThe mechanical properties of the axial muscles vary along the length of a fish's body. This variation in performance correlates with the expression of certain muscle proteins. Parvalbumin (PARV) is an important calcium binding protein that helps modulate intracellular calcium levels which set the size and shape of the muscle calcium transient. It therefore has a central role in determining the functional properties of the muscle. Transcript data revealed eight specific isoforms of PARV in common carp (Cyprinus carpio)skeletal muscle which we classified as α1 and β1–7. This study is the first to show expression of all eight skeletal muscle PARV isoforms in carp at the protein level and relate regional differences in expression to performance. All of the PARV isoforms were characterised at the protein level using 2D-PAGE and tandem mass spectrometry. Comparison of carp muscle from different regions of the fish revealed a higher level of expression of PARV isoforms β4 and β5 in the anterior region, which was accompanied by an increase in the rate of relaxation. We postulate that changes in specific PARV isoform expression are an important part of the adaptive change in muscle mechanical properties in response to varying functional demands and environmental change.

The common carp (Cyprinus carpio) has a well-developed capacity to modify muscle properties in response to changes in temperature. Understanding the mechanisms underpinning this phenotypic response at the protein level may provide fundamental insights into the molecular basis of adaptive processes in skeletal muscle. In this study, common carp were subjected to a cooling regimen and soluble extracts of muscle homogenates were separated by 1-D SDS-PAGE and 2-DE. Proteins were identified using MALDI-TOF-MS and de novo peptide sequencing using LC-MS/MS. The 2-D gel was populated with numerous protein spots that were fragments of all three muscle isoforms (M1, M2 and M3) of carp creatine kinase (CK). The accumulation of the CK fragments was enhanced when the carp were cooled to 10 degrees C. The protein changes observed in the skeletal muscle of carp subjected to cold acclimation were compared to changes described in a previous transcript analysis study. Genes encoding CK isoforms were downregulated and the genes encoding key proteins of the ubiquitin-proteasome pathway were upregulated. These findings are consistent with a specific cold-induced enhancement of proteolysis of CK.

Mouse urine contains highly polymorphic major urinary proteins that have multiple functions in scent communication through their abilities to bind, transport and release hydrophobic volatile pheromones. The mouse genome encodes for about 20 of these proteins and are classified, based on amino acid sequence similarity and tissue expression patterns, as either central or peripheral major urinary proteins. Darcin is a male specific peripheral major urinary protein and is distinctive in its role in inherent female attraction. A comparison of the structure and biophysical properties of darcin with MUP11, which belongs to the central class, highlights similarity in the overall structure between the two proteins. The thermodynamic stability, however, differs between the two proteins, with darcin being much more stable. Furthermore, the affinity of a small pheromone mimetic is higher for darcin, although darcin is more discriminatory, being unable to bind bulkier ligands. These attributes are due to the hydrophobic ligand binding cavity of darcin being smaller, caused by the presence of larger amino acid side chains. Thus, the physical and chemical characteristics of the binding cavity, together with its extreme stability, are consistent with darcin being able to exert its function after release into the environment.