Proteins locally secreted in the digestive system
There are 94 proteins predicted to be locally secreted in the digestive system based on manual literature analysis and data analysis. The digestive system comprises of the digestive tract as well as tongue, salivary glands, pancreas, liver and gallbladder. Digestion of food begins in the mouth by enzymes in the saliva produced by salivary glands. Saliva also contains mucin that lubricates and protects the oral mucosa. Movement of the tongue facilitates chewing and swallowing of food. Food is transported from the mouth to the stomach via the esophagus. When food reaches the stomach, it is further processed by several digestive enzymes and hydrochloric acid secreted by cells lining the gastric wall. The decrease in pH resulting from hydrochloric acid release is essential for the activity of the gastric digestive enzymes. After entering the duodenum, the acidic contents from the stomach are neutralized by fluids secreted from the duodenum and pancreas. In addition, bile produced in the liver and concentrated in the gallbladder, as well as pancreatic enzymes, are emptied into the small intestine where they further digest food particles into molecules that are absorbed by intestinal epithelial cells. Mucosal surfaces throughout the digestive tract are protected by a mucous gel that contains mucin. Secreted antibacterial proteins also have a key role in the protection of the mucosal surfaces. They are produced by various glandular cells in the digestive system.
Functions of proteins locally secreted in the digestive system
All proteins that are secreted to digestive system were classified according to function based on Uniprot molecular function and biological processes keywords. The annotations were prioritized in the following hierarchy: Blood coagulation, Complement pathway, Acute phase, Cytokine, Hormone, Neuropeptide, Growth factor, Receptor, Lectin, Transport, Developmental protein, Defence, Enzyme, Enzyme inhibitor, Transcription, Immunity, Cell adhesion. Each gene was assigned one function. Our analysis shows that 26 proteins secreted in the digestive system lack an annotated function (Figure 1). However, among the remaining 68 proteins, we could identify several proteins with various functions including enzymes (n=38) that catalyze the breakdown of fat, carbohydrates, proteins and RNA, as well as the generation of antimicrobial substances, enzyme inhibitors (n=7) that regulate digestion and other physiological processes, and antimicrobial and cytotoxic substances involved in immune defense (n=4). Other secreted proteins are associated with the transport of chloride and vitamins across the intestinal epithelium, cell-to-cell communication and development.
Figure 1. Number of proteins that are locally secreted to digestive system, categorized according to function. Annotation was based on Uniprot molecular function and biological processes keywords. Each bar is clickable and gives a search result of proteins that belong to the selected category.
Tissue specificity and tissue distribution classification
The genes encoding proteins locally secreted in the digestive system were further analyzed with regard to mRNA expression and categorized according to tissue specificity and tissue distribution. A vast majority of genes showed either tissue enriched (n=81) or group enriched (n=8) mRNA expression, i.e. either at least four-fold higher mRNA level in one tissue or in a group of two to five tissues compared to all other tissues (Figure 2). A small subset of genes (n=5) were tissue enhanced, i.e. showing four-fold higher average mRNA levels in one or more tissues compared to the mean mRNA level. Furthermore, for most genes, mRNA was detected either in a single tissue or in a few tissues (less than 30 percent of the analyzed tissues). Few genes (n=47) were detected in over 30 percent of the analyzed tissues (Figure 3).
Figure 2. Number of genes encoding proteins that are locally secreted to digestive system, categorized according to tissue specificity. Categories include: tissue enriched, defined as mRNA level in one tissue at least four-fold higher than in all other tissues; group enriched, defined as four-fold higher average mRNA level in a group of two to five tissues compared to all other tissues; tissue enhanced, defined as four-fold higher average mRNA level in one or more tissues compared to the mean mRNA level of all tissues; expressed in all, defined as ≥ 1 nTPM in all tissues; and not detected, defined as < 1 nTPM in all tissues.
Figure 3. Number of genes encoding proteins that are locally secreted to digestive system, categorized according to tissue distribution. Categories include: detected in all, defined as n=100%; detected in many, defined as 31%=< n <100%; detected in some, defined as 1< n <31%; detected in single defined as single n=1; and not detected, n=0.
Origin of proteins locally secreted in the digestive system
The analysis of gene expression showed that most tissue enriched proteins annotated as locally secreted in the digestive system are produced either in the pancreas (n=29) or in salivary glands (n=26) (Figure 4). Remaining proteins were encoded by genes with mRNA enriched in either stomach (n=12) or in the intestinal tract (n=12).
Figure 4. Number of tissue enriched genes encoding proteins that are locally secreted to digestive system, according to the tissue with highest mRNA level. Each bar is clickable and gives a search result of proteins that belong to the selected category.
Examples of proteins locally secreted in the digestive system
Saliva produced by the salivary gland has a key role in the digestion of food as well as protection of the mucosal surface of the mouth. Amylases are a group of digestive enzymes that catalyze the first step in the chemical breakdown of dietary starch and glycogen. Amylase alpha 1A (AMY1A) is salivary gland specific and is a key component of the saliva produced by serous glandular cells of the salivary gland. Mucinous glandular cells secrete saliva rich in mucin that lubricates and protect the mouth from microbes. A salivary gland enriched member of the mucin protein family is mucin 7 (MUC7). Another protein important for the clearance of microbes is the antimicrobial peptide histatin 1 (HTN1). HTN1 protects againts bacteria, fungi and helps wounds to heal.
The exocrine glandular cells of the pancreas secrete various digestive enzymes. One of them is amylase alpha 2A (AMY2A), and just as AMY1A and other amylases, it is involved in the digestion of carbohydrates. An enzyme involved in protein digestion is chymotrypsin like elastase family member 3A (CELA3A), a member of the elastase family of serine proteases. It preferentially cleaves proteins after alanine residues. Carboxypeptidases are another type of enzymes produced exclusively by the pancreas. Carboxypeptidase A2 (CPA2) targets aromatic C-terminal residues of proteins.
Proteins are also digested in the stomach by the stomach-specific enzyme pepsin. Pepsinogen 3 (PGA3) is one of the precursors of pepsin that is secreted by gastric chief cells and then cleaved to generate the active form of the enzyme. Chief cells also secrete a protein involved in the breakdown of fat, lipase F (LIPF), which is a stomach-specific member of the lipase family of proteins. Another type of gastric glandular cells, parietal cells, produce hydrochloric acid, in response to stimulation from the hormone gastrin (GAST). GAST is secreted by G-cells in the gastric epithelium.
One of the proteins secreted in the intestines is chloride channel accessory 1 (CLCA1). It is a transport protein that aids the absorption of molecules across the intestinal epithelia. The intestines also produce antimicrobial peptides, such as defensin 5 (DEFA5), which is secreted by Paneth cells in the intestinal epithelium. Other members of the defensin family of proteins are found in neutrophils, respiratory tract, urinary tract and vagina.
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