Proteomic profiling of white muscle from freshwater catfish Rita rita

Physiological Responses to Acute Heat Stress in Rohu, Labeo rohita: Insights from Liver Proteomics

Heat stress is a major problem in aquaculture species, causing changes in physiology such as decreased feed intake, growth rate, reproduction, and internal cellular damage, thereby affecting fish's health. The effects of an acute heat stress simulating a daily rise and fall in temperature on summer days were evaluated in the liver proteome of rohu (Labeo rohita) fingerlings in the present study. The fish maintained at 30 °C were gradually exposed to a higher temperature of 36 °C at an increment rate of 1 °C per 1.5 h, and after 3 h at that temperature, it was gradually reduced to 30 °C. The liver tissue samples were collected at 5 am, 5 pm, and 5 am the next day from the exposed and control fish. Protein samples were prepared from the liver tissues, and the extracted proteins were compared using 2-dimensional (2D) gel electrophoresis (2DGE) and mass spectrometry (MS) using a MALDI-TOF/TOF mass spectrometer. A total of 44 differentially expressed protein spots were visualized in 2D gel analysis from heat stress exposed fish at three time points, out of which 21 proteins including one hypothetical protein could be identified by MS. The abundance of five selected differentially expressed proteins (DEPs) was validated using qPCR. The majority of DEPs were found to be involved primarily in lipid, protein and energy metabolism, immune system regulation, cytoskeletal stability, and ROS management. The findings of this study would help in the development of strategies to mitigate heat stress in L. rohita.

Age-specific changes in the serum proteome of female anadromous, hilsa Tenualosa ilisha: a comparative analysis across developmental stages

Introduction

The proteome profile of the female Tenualosa ilisha (Hamilton, 1822), a species of great ecological and economic importance, across various age groups was investigated to comprehend the functional dynamics of the serum proteome for conservation and aquaculture, as well as sustain the population.

Methods

Advanced liquid chromatography-tandem mass spectrometry LC-MS/MS-based proteomic data were analysed and submitted to the ProteomeXchange Consortium via PRIDE (PRoteomics IDEntifications database). Bioinformatics analysis of serum proteome have been done and it showed different proteins associated with GO Gene Ontology () terms, and the genes associated with enriched KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways (such as phagosome, mTOR, Apelin signalling pathways, herpes simplex virus) implicated in immune responses.

Results

The expression levels of important immunological proteins, such as those involved in cellular defence and inflammatory responses, were significantly different age-dependently. In this study, we annotated 952, 494, 415, and 282 proteins in year classes IV, III, II, and I Hilsa, respectively, and analysed their Protein-Protein Interaction (PPI) networks based on their functional characteristics. From year classes I to IV, new proteins appeared and were more than three-fold. Notably, class I hilsa displayed a lower abundance of proteins than class IV hilsa.

Discussion

This is the first study, to the best of our knowledge, to report the analysis of the serum proteome of hilsa at different developmental stages, and the results can help improve the understanding of the mechanisms underlying the different changes in protein enrichment during migration in hilsa. This analysis also offers crucial insights into the immune system for hilsa conservation and management.

LC-MS/MS based characterisation and differential expression of proteins in Himalayan snow trout, Schizothorax labiatus using LFQ technique

Molecular characterization of fish muscle proteins are nowadays considered as a key component to understand the role of specific proteins involved in various physiological and metabolic processes including their up and down regulation in the organisms. Coldwater fish specimens including snow trouts hold different types of proteins which help them to survive in highly diversified temperatures fluctuating from 0 to 20 °C. So, in current study, the liquid chromatography mass spectrometry using label free quantification technique has been used to investigate the muscle proteome profile of Schizothorax labiatus. For proteomic study, two weight groups of S. labiatus were taken from river Sindh. The proteomic analysis of group 1 revealed that a total of 235 proteins in male and 238 in female fish were recorded. However, when male and female S. labiatus were compared with each other on the basis of spectral count and abundance of peptides by ProteinLynx Global Server software, a total of 14 down-regulated and 22 up-regulated proteins were noted in this group. The highly down-regulated ones included homeodomain protein HoxA2b, retinol-binding protein 4, MHC class II beta chain and proopiomelanocortin while as the highly expressed up-regulated proteins comprised of gonadotropin I beta subunit, NADH dehydrogenase subunit 4, manganese superoxide dismutase, recombinase-activating protein 2, glycosyltransferase, chymotrypsin and cytochrome b. On the other hand, the proteomic characterisation of group 2 of S. labiatus revealed that a total of 227 proteins in male and 194 in female fish were recorded. When male and female S. labiatus were compared with each other by label free quantification, a total of 20 down-regulated and 18 up-regulated proteins were recorded. The down-regulated protein expression of group 2 comprised hepatic lipase, allograft inflammatory factor-1, NADH dehydrogenase subunit 4 and myostatin 1 while the highly expressed up-regulated proteins included glycogen synthase kinase-3 beta variant 2, glycogen synthase kinase-3 beta variant 5, cholecystokinin, glycogen synthase kinase-3 beta variant 3 and cytochrome b. Significant (P < 0.05) difference in the expression of down-regulated and up-regulated proteins was also noted between the two sexes of S. labiatus in each group. According to MS analysis, the proteins primarily concerned with the growth, skeletal muscle development and metabolism were down-regulated in river Sindh, which indicates that growth of fish during the season of collection i.e., winter was slow owing to less food availability, gonad development and low metabolic activity. While, the proteins related to immune response of fish were also noted to be down-regulated thereby signifying that the ecosystem has less pollution loads, microbial, pathogenic and anthropogenic activities. It was also found that the proteins involved in glycogen metabolism, reproductive and metabolic processes, particularly lipid metabolism were up-regulated in S. labiatus. The significant expression of these proteins may be connected to pre-spawning, gonad development and use of stored food as source of energy. The information generated in this study can be applied to future research aimed at enhancing food traceability, food safety, risk management and authenticity analysis.

Seasonal analysis of food items and feeding habits of endangered riverine catfish Rita rita (Hamilton, 1822)

This investigation presents the food and feeding activity of and endangered riverine catfish Rita rita, during February 2017-January 2018. A total of 225 fish individuals was analyzed for stomach contents by characterizing the dominant food items and morphometric features. The results divulged ten major food items consumed, preferably fish scales and eggs, teleost fishes, copepods, cladocerans, rotifers, and mollusks. Total length and body weight of fish varied between 9-34 cm (20.53 ± 6.90 cm) and 10-400 g (9125.94 ± 102.07 g), respectively. The index of relative importance (IRI%) showed the importance of rotifers over the other food items. Morisita's index of diet overlap indicated seasonal variations in catfish diets with summer and monsoon displaying the least overlap, while maximum overlap during monsoon and winter seasons. The non-metric multidimensional scaling (nMDS) indicated the close association between the food items available during summer and winter seasons with a significant difference among the seasons (ANOSIM, R = 0.638, P = 0.013). Levin's niche breadth index arranged in the order of 0.88>0.81>0.78>0.63>0.43 for the size classes of V, IV, III, II and I, respectively. The PCA explained 95.39% of the total variance among the food items and fish size groups. Small-sized fish individuals displayed a greater correlation with food items suitable for their mouth size. In conclusion, the variety and frequency of food items recorded indicated considerable feeding plasticity and opportunistic feeding behavior with a shift from carnivorous to omnivorous feeding nature. This study could render useful information on the food and feeding habits of R. rita and provide background for preparing its diet for future aquaculture practices.

Can proteomics contribute to biomonitoring of aquatic pollution? A critical review

Aquatic pollution is one of the greatest environmental problems, and therefore its control represents one of the major challenges in this century. In recent years, proteomics has emerged as a powerful tool for searching protein biomarkers in the field of pollution biomonitoring. For biomonitoring marine contamination, there is a consensus that bivalves are preferred organisms to assess organic and inorganic pollutants. Thus, the bivalve proteome was intensively studied, particularly the mussel. It is well documented that heavy metal pollution and organic chemicals altered the structural proteins causing degradation of tissues of molluscs. Also, it is well known that proteins involved in stress oxidative such as glutathione and enzymes as catalase, superoxide dismutase or peroxisomes are overexpressed in response to contaminants. Additionally, using bivalves, other groups of proteins proposed as pollution biomarkers are the metabolic proteins. Even though other marine species are used to monitor the pollution, the presence of proteomic tools in these studies is scarce. Concerning freshwater pollution field, a great variety of animal species (fish and crustaceans) are used as biomonitors in proteomics studies compared to plants that are scarcely analysed. In fish species, proteins involved in stress oxidative such as heat shock family or proteins from lipid and carbohydrate metabolism were proposed as candidate biomarkers. On the contrary, for crustaceans there is a lack of proteomic studies individually assessing the contaminants. Novel scenarios, including emerging contaminants and new threats, will require proteomic technology for a systematic search of protein biomarkers and a greater knowledge at molecular level of those cellular pathways induced by contamination.

Expression patterns of heat shock protein genes in Rita rita from natural riverine habitat as biomarker response against environmental pollution

River pollution is one of the principal environmental concerns and biomonitoring tools can play an important role in pollution assessment in the riverine environment. Heat shock proteins (Hsps) have been found to be suitable tools for monitoring stress response. In the present study, expression analyses of hsp genes (hsp27, hsp47, hsp60, hsp70, hsc70, and hsp90) and selected hsp-regulatory genes (hsf1, hyou1, ask1, jnk) were carried out by RT-qPCR in catfish Rita rita collected from selected stretches of river Ganga to investigate changes in their expression patterns as biomarker response. Water quality characteristics were measured in terms of physico-chemical characteristics (DO, BOD, COD, pH, conductivity), element profile (arsenic, mercury, cadmium, lead, chromium, zinc, copper) and persistent organic pollutants (POPs; HCH, DDT, aldrin, endosulphan, heptachlor). Water quality index was calculated and sampling sites were categorized as good/medium/bad. Multivariate analysis was carried out taking the water quality parameters and the fold changes in hsp gene expression as variables, which showed that hsp47 and hsp70b correlated well with BOD, an indicator of organic pollution. To identify the organic pollutant(s) which could be influencing the expression of hsps, again multivariate analysis was employed taking concentration of POPs and fold changes of hsps, which showed up-regulation of hsp47 and hsp70b (HSP72i) correlated well with concentrations of aldrin and HCH. Synergistic effects of these POPs could be responsible for the up-regulation of said hsps, although individually present in low concentration; thus, indicating synergistic effect of the POPs on hsp47 and hsp70b up-regulation as biomarker response.

Expression patterns and mutation analysis of p53 in fish Rita rita from polluted riverine environment

The present study was undertaken to investigate the alterations in gene expression patterns and for mutation analysis of p53 in the riverine catfish Rita rita collected from polluted riverine habitat. The partial p53 gene sequence of Rita rita generated showed a high degree of similarities with the DNA binding domains of fishes, mice and human. Transcriptomic analysis, carried out by quantitative real-time Polymerase Chain Reaction (RT-qPCR), showed significant down-regulation of p53 in fishes collected from most of the polluted stretches. Similar trend in protein abundance was observed by western blot analysis. Down-regulation of p53 was more pronounced in gill than liver. Expression patterns of p53 suggest that exposure to a multitude of contaminants in the natural riverine ecosystem could suppress the expression of p53. Genomic DNA showed a low stained smear pattern upon electrophoresis, with no evidence of DNA fragmentation. For mutation analysis PCR-SSCP followed by sequence analysis was carried out, which identified eight mutations; two at codon level and six missense mutations in the DNA binding domain IV and V. Secondary structure prediction showed that these mutations could lead to impairment of protein structure. Thus, the present study indicated that aquatic pollution has impacted these lower vertebrates which are reflected by the down-regulation of tumor suppressor protein (p53) in majority of the stretches studied.