1. Introduction
Aerobic
animals use oxygen to generate energy through oxidative phosphorylation
within mitochondria. Currently, aquatic ecosystems are increasingly
under pressure from pollutants, nutrient enrichment, and global warming,
all of which more increase the risk of hypoxia in water
(Mandicet al. 2015). Therefore, aquatic organisms are usually exposed
to different concentrations of dissolved oxygen.
A
severe and sudden hypoxia can be fatal for hypoxia-sensitive fish.
Revealing the molecular mechanism of fish hypoxia adaptation will help
us find the hypoxic marker caused by environmental stress (Abdelrahman
et al. 2017).
In order to maintain
organism function and homeostasis in
a hypoxic environment, aquatic organisms, including fishes, respond by
various behavioral and physiological adjustments, e.g., decreasing
swimming rate, increasing respiration rate, increasing oxygen supply,
and reducing oxygen consumption (Sappalet al. 2016; Zhong et al.2009). These process depends on the division and cooperation among
tissues in fishes, such as liver, muscle, brain, heart, gill. Relevant
research results show that there are differences in the sensitivity and
tolerance of different tissues, indicating that the tissue-specific
expression pattern reflects the different metabolic effects of tissues
during hypoxia (Zhu et al. 2013).
For example, fish brain and heart
showed fewer examples of down-regulation compared with muscle, in
keeping with the need for sustained activity
(Gracey et al. 2001;
Lardon et al. 2013). The different
patterns may also be related to the extent of the hypoxic insult that
each tissue experiences. For example, fish heart receives blood directly
from the gills and thus will have a better oxygen supply than other
tissues (Everett et al. 2012;
Ju et al. 2007).
Now, various methods in fish were applied for studies of the hypoxia
molecular mechanisms, e.g., investigations for
transcriptional changes using
qRT-PCR (Chen et al. 2012;
Wang et al. 2015), transcriptome
(Beck et al. 2016;
Gong et al. 2020;
Yang et al. 2018), and changes in
protein using 2D-DIGE (Dowd et al.2010; Smith et al. 2009;
Wulff et al. 2012). Biological
phenomena induced by environmental stress are changeable and complex,
which is also accompanied by complicated regulation of
miRNA/gene/protein expression. Multiple omics are combination of two or
more omics methods, and can avoid the incomprehensive conclusions of
single-omics (Sun et al. 2018).
Unfortunately, the study of the fishes responding mechanism undergo
hypoxia using multi-omics is negligible, which vastly hinders the
comprehensive understanding of this biological phenomenon.
Pelteobagrus vachelli has become a popular commercial fishes in
Asia because of its relatively high yield and an affordable price for
consumers (Guosong et al. 2017).
However, due to its low oxygen threshold and high oxygen consumption
rate, this species is only found in the rivers. A sudden lack of oxygen
can result in mortality and finally cause the pond turnover
(Zhang et al. 2016a). These
properties indicate that P. vachelli is not only an important
aquaculture variety, but also a potential model fishes for studying the
molecular mechanisms of hypoxia. Recently, the miRNA-mRNA regulatory
network has been shown to respond to hypoxia in livers ofMegalobrama amblycephala (Sun et
al. 2017) and P. vachelli (Zhanget al. 2016b). This suggests that the HIF-1 signaling may be
involved in fish hypoxic molecular adaptation, which is often regulated
and controlled by the physiological changes. Also, we conducted iTRAQ
proteomic analysis in P. vachelli livers to uncover hypoxic
responsive proteins involved in diverse biological pathways, e.g.,
peroxisome, glycolysis, PPAR signaling, lipid and amino acid metabolism
(Zhang et al. 2017).
At
present, relative to other tissues, studies on the mechanism of fish
muscle, the largest tissue, response to hypoxia are relatively scarce.
Therefore, we characterize transcriptomic,
miRNAomic, proteomic and metabolomic
changes of P. vachellimuscles under environmental hypoxia simultaneously (Fig. 1 ),
combined with the previous studies on P. vachelli liver. Our
findings aim to offer deeper insights into
tissue-specific patterns of
expression induced by environmental hypoxia,
on
the other hand the methods and study design can be used to analyze
markers to profile other species undergo hypoxic environmental stress.