What is the difference between protease and peptidase

Acidobacteria encoded the highest mean number of secreted peptidases per genome, with a large relative increase in the number of secreted metallopeptidases and a concomitant decrease in the number of cysteine peptidases compared to other bacterial phyla Figure 2.

Figure 7. Distribution of secreted peptidases super-families across the bacterial phylogenetic tree. Outer tracks show the copy numbers of genes from each secreted peptidase super-family in each genome. Genomes of the Bacteroidetes and Actinobacteria phyla encoded high numbers of secreted peptidases and exhibited strong within-phylum distribution patterns related to finer-scale relationships Figure 7.

For the Bacteroidetes , serine and metallopeptidases were dominant and well-conserved in presence and copy number across all species Figure 8A. By contrast, cysteine peptidases seemed to be more abundant i. Figure 8. Distribution of strain-specific secreted peptidases across A Bacteroidetes and B Actinobacteria taxa. The middle tracks show the copy number of genes from each secreted peptidase super-family in each genome.

In the Actinobacteria , differences among clades were more strongly related to the numbers of peptidase genes than to the types of secreted peptidases Figure 8B but were still highly correlated with the environmental microhabitat in which a taxon was found.

Secreted peptidase diversity varied between Archaea and Bacteria , suggesting the potential for specialized peptidase functions and optimization among taxa.

This variation may be related to differences in the catalytic residues of the active site; these biochemical differences may provide specific adaptive advantages to different taxa under varying environmental conditions. As a general hydrolytic mechanism, a nucleophilic amino acid residue or water molecule is activated to attack a peptide carbonyl group, cleaving a peptide bond.

In the case of serine, cysteine, and threonine peptidases, the histidine residue of a catalytic triad activates the serine, cysteine, or threonine residue, which then serves as the nucleophile that splits the peptide bond Rao et al. Alternatively, for aspartic and metallopeptidases the aspartic acid residue or an enzyme-bound metal cofactor activates a water molecule to act as the nucleophile for the hydrolysis Wu and Chen, ; Theron and Divol, Bacterial species generally possess more secreted peptidases per genome and have a more diverse repertoire of secreted peptidase families compared to archaeal species Figures 2 , 3.

This may confer greater flexibility on Bacteria to generate different types of extracellular proteolytic enzymes in response to specific environmental conditions depending on their demand for carbon and nitrogen, resulting in consistently high levels of overall peptidase activity in situ. This also suggests that Bacteria could be more competitive in obtaining organic nitrogen from the environment compared to Archaea. Empirical studies have implicated Bacteria to be the dominant contributor to proteolytic activity in soils Watanabe and Hayano, , ; Katsuji et al.

Our analysis shows that these genera also have a high richness and abundance of secreted peptidases, consistent with their high soil peptidase activities. At the super-family level, much of the variability in peptidase profiles between genomes of prokaryotic taxa was linked to differences in counts of less common peptidases, namely aspartic peptidases in Archaea and threonine peptidases in Bacteria Figures 1 , 3.

Differences in the complement of secreted peptidases may reflect their adaptation to environmental conditions, such as temperature or pH. Serine, cysteine, and metallo- peptidases are generally optimized and active at neutral to alkaline pH Rao et al. Our analyses indicate that these enzymatic pH optima reflect the environments in which they are found.

For example, three peptidase families — A05, A37, and S53 — were enriched in archaeal acidophile genomes Figure 6. All three of these peptidase families have been shown to have optimal endopeptidase activities at low pH Rawlings et al. Additionally, peptidases of the S53 family appear to be novel endopeptidases within the serine peptidase super-family.

These enzymes encode a catalytic triad consisting of Glu, Asp, and Ser residues, as well as an additional Asp residue in the oxyanion hole of the active site Wlodawer et al. This active site arrangement stands in contrast to the traditional Asp, His, Ser triad observed in the more common serine S08 peptidases, and effectively relies on two additional acidic residues for activity. These active site arrangements likely relate to the activities of S08 and S53 peptidases in different pH environments, and may account for the observed strong negative correlation of the presence of S08 peptidases within acidophilic genomes.

Therefore, the variation in the diversity of peptidase super-families encoded by microbes appears to be at least partially influenced by optimization of catalytic site to specific environmental conditions. In Bacteria , there is a significant difference between the secreted peptidase composition of Gram-positive and Gram-negative bacteria. These two groups of Bacteria differ in cell wall structure Vollmer et al.

The distinction between these enzyme secretion strategies may influence the types of extracellular proteolytic enzymes encoded by these two groups of Bacteria. The conservation of secreted peptidase complements between pairs of archaeal and bacterial taxa was found to have a moderate positive correlation with phylogenetic relatedness across the prokaryotic tree of life.

For both Archaea and Bacteria this relationship weakens rapidly as phylogenetic distance increases and, for bacterial taxa at least, the relationship is only significant up to approximately the family-level taxonomic equivalent of phylogenetic similarity.

These patterns may be due in some part to horizontal gene transfer of peptidases, which may act to conserve features between more closely related taxa that more commonly exchange genes via this mechanism Lawrence and Hendrickson, ; Choi and Kim, As discussed below, this conservation may also be partially attributed to a confounding correlation between phylogeny and environmental microhabitat of the taxa considered, given that phylogenetically-related taxa often inhabit grossly similar environments.

Thus, our analyses are necessarily limited by the definition of microhabitat used here, which may insufficiently define the true microhabitats of each taxon and the corresponding relationship to functional specialization of peptidase families within those habitats. Despite this potential limitation, these results stand in contrast to the insignificant relationship observed for glycoside hydrolase GH profiles and phylogenies of prokaryotes that was defined using a similar approach Berlemont and Martiny, Various technical and analytical reasons could account for this discrepency e.

However, stronger conservation of peptidase vs. GH content in genomes could also indicate biologically-driven differences in selective pressures on the different enzymatic types, despite their similar general functional roles in modifying cellular components and obtaining resources via secreted degradative enzymes. Further work will be needed to better define the roles of these important enzymes in speciation and competition in the environment.

Most secreted peptidase families encoded in bacterial genomes were determined to have significant phylogenetic signals in their distribution patterns across taxa. These findings agree with previous studies that found conservation of prokaryotic traits that are governed by multiple genes or metabolic pathways e. Non-random distributions were also observed for most super-families when compared to both archaeal and bacterial phylogenies Supplementary Tables S4 , S5.

Here, more negative D -values, which are indicative of extreme phylogenetic clustering, were typically observed for less common peptidases e. When the conservation and variation of genome-encoded secreted peptidases was examined within more specific bacterial clades e.

Generally speaking, Bacteroidetes taxa commonly associated with aquatic or soil environments, such as Cytophagaceae , Sphinobacteriaceae , and Flavobacteriaceae , encoded more total peptidases compared to animal-associated Bacteroidetes , such as Bacteroides and Prevotella.

The Flavobacteriaceae include taxa with different lifestyles and genome sizes, and which are common inhabitants of terrestrial and marine ecosystems. Their ability to successfully compete in such oligotrophic environments may be dependent on their capacity to quickly degrade proteinaceous material to obtain nitrogen as a supplement to their well-established specialization of using carbohydrates for energy and as a carbon source Bryson et al.

This may account for the enriched proteolytic enzyme repertoire observed for these taxa, which is comprised of many outer membrane-associated and extracellular peptidases Kolton et al. By contrast, host-associated Prevotella species present inside the rumen Wallace et al.

Similar to these trends, Actinobacterial families common to soil and aquatic environments Streptomycetaceae , Pseudonocardiaceae , Nocardiaceae , Micromonosporaceae , and Actinoplanaceae were also found to have a greater diversity and abundance of peptidases encoded in their genomes compared to animal-associated taxa.

This observation agrees well with our current understanding of the ecology of Actinomycetes and their prodigious role as organic matter decomposers in nutrient-limited environments such as soils and freshwaters Wink et al. Streptomyces species are abundant in terrestrial ecosystems and are well-known for their ability to use a wide variety of insoluble environmental substrates such as animal, plant, fungal, and microbial biomass by diverse extracellular enzymes, including peptidases Chater et al.

Interestingly, some secreted peptidases from Streptomyces , which are strictly regulated by their own inhibitors, are to cannibalize their own mycelial biomass in order to support aerial growth and sporulation when needed Chater et al.

With a rich repertoire of keratinases mostly serine and metallo- peptidases , some Streptomyces can degrade keratin, an insoluble structural and highly polymerized protein that is commonly found in the outer covering of many animals Gupta and Ramnani, ; Chater et al. In other cases, extracellular peptidases from Streptomyces may also play a role as an activating mechanism for other secreted proenzymes, such as nucleases, cellulases, and xylanases Chater et al.

An exception within the soil-associated Actinobacteria with regard to secreted peptidase content are taxa within the Frankiaceae family, which are diazotrophic and can be endosymbionts of actinorhizal plants.

Mastronunzio et al. This pattern does not hold for rhizobia, however, which is a group of diazotrophic Alphaproteobacteria that form root nodules in legumes and that encode a much richer collection of secreted peptidases compared to Frankiaceae or other non-N 2 -fixing Alphaproteobacteria. Interestingly, rhizobia are known to fix nitrogen only when in a symbiosis with plants because they lack an endogenous oxygen protection mechanism for the nitrogenase enzyme that catalyzes the nitrogen fixation Pawlowski and Bisseling, Thus, possessing an abundant collection of extracellular peptidases might be a strategy for free-living rhizobia to scavenge organic nitrogen and carbon from proteins.

In contrast, Frankia species maintain their ability to fix atmospheric nitrogen to meet their nitrogen demand when free-living, potentially obviating their need to secrete peptidases to scavenge organic nitrogen from the environment Pawlowski and Bisseling, ; Norman and Friesen, Most animal-associated Actinobacteria were found to have a lower abundance of secreted peptidases in comparison with those taxa associated with aquatic or soil environments.

In this environment, proteolytic activity predominantly arises from peptidases in human breast milk e. Our analysis Figure 8 showed that Bifidobacteriaceae taxa have a limited potential to break down proteins, which might reflect the high abundance of host-derived peptidases that generate bioavailable nitrogen within the gut. Conversely, another group of animal-associated Actinobacteria , the Mycobacteriaceae , possess large numbers of secreted peptidase genes in their genomes.

Most Mycobacterium species are pathogenic e. Other peptidases in Mycobacteria , such as MycP1 of the S08 family, cleave proteins of the virulent secretion system as part of the infection process Abdallah et al.

Collectively, these examples support the potential role of environmental microhabitat in selecting for peptidase functions, with the general theme that host-associated bacteria tend to encode fewer secreted peptidases than those taxa that are free-living.

There are exceptions to this pattern, however, which appear to be linked to specialized traits of the microbes e. Our analysis of peptidase diversity has practical implications for microbial ecology studies of protein degradation. First, our analysis of the microbial potential for secreted peptidase production is a foundation for subsequent research applying transcriptomic or proteomic approaches to determine how this potential is realized by the secretion of peptidases under specific environmental conditions.

Second, the current oligonucleotide primers designed to amplify peptidases from environmental DNA using PCR focus on specific peptidase families that are encoded by limited microbial taxa. For example, the npr primers are able to detect neutral metallopeptidases of the M04 family primarily associated with Bacillus species 23 rd most abundant peptidase family , primers for sub detect the subtilisin-like S08 peptidase family associated with Bacillus species 9th in abundance , and apr primers can identify only alkaline metallopeptidases of the M10 family from Pseudomonas fluorescens 57th in abundance Bach and Munch, ; Tsuboi et al.

Therefore, there is a need to design primer sets that are more universal or target a larger diversity of microbial secreted peptidases and that focus on the more abundant families of secreted peptidases e. TN and DM conceived of the presented idea. TN extracted and processed data from other databases and implemented the computational and statistical analyses and took the lead in writing the manuscript. DM and RM supervised the findings of this work. All authors provided critical feedback and helped to shape the research, analysis and manuscript.

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. Abdallah, A. Type VII secretion — Mycobacteria show the way. Microbiol 5, — Allison, S. Nitrogen alters carbon dynamics during early succession in boreal forest. Soil Biol. Arnosti, C. Contrasting patterns of peptidase activities in seawater and sediments: an example from Arctic fjords of Svalbard.

One of the great things about being a protein biochemist is you can express and purify your own stocks of the ones you use a lot. The StrepTag is an affinity tag that I can use to bind to a streptactin column to help me purify it. Sometimes this can be annoying because it can prevent you from easily de-tagging your protein if this is the case you might want to try switching the tag to the other end of the protein where it might be more accessible.

In a technique called limited proteolysis, you add a small amount of endoprotease to a protein and see where it gets cut — you take samples over time to see which areas are the most vulnerable and therefore likely most accessible.

And the difference in their names really does reflect key differences in their make-up. If you want to cut single-stranded regions around hybrids, go for S1 nuclease, which can cut up single-stranded DNA or RNA though it prefers DNA while leaving alone double-stranded regions — great for seeing where probes bind and stuff. In the lab, non-specific endonucleases can be useful for removing nucleic acids during protein purification — they can really gunk things up.

Moreover, there are two types of peptidases based on the type of terminus they hydrolyze. Basically, they are aminopeptidases, which hydrolyze terminal peptide bonds in the amino-terminal, and carboxypeptidases, which hydrolyze terminal peptide bonds in the carboxy-terminal. Furthermore, aminopeptidases occur in the brush border of the small intestine. On the other hand, carboxypeptidases occur in the pancreatic juice of the digestive system. Protease refers to an enzyme that breaks down proteins and peptides, w hile peptidase refers to an enzyme that breaks down peptides into amino acids.

Thus, this is the main difference between protease and peptidase. Protease is a hydrolytic enzyme that hydrolyzes peptide bonds, while peptidases are a type of proteases. Besides, the two types of proteases are endopeptidases and exopeptidases while peptidase is an exopeptidase. Moreover, endopeptidases hydrolyze internal peptide bonds, while peptidases hydrolyze peptide bonds at the end. Also, another difference between protease and peptidase is that endopeptidases prefer intact proteins, while peptidases prefer small peptides.

You can download PDF version of this article and use it for offline purposes as per citation notes. Accessed 15 Sept. Public Domain via Commons Wikimedia 2. Samanthi Udayangani holds a B.

Degree in Plant Science, M. Your email address will not be published. Figure Protease. Figure Peptidase Action. Leave a Reply Cancel reply Your email address will not be published. Protease vs Peptidase. Proteases are enzymes that cleave the peptide bond in proteins. Peptidases are a type of protease that is capable of cleaving the end terminals of the peptide chain.